WorldWideScience

Sample records for biological imaging experiments

  1. Tracer tests and image analysis of biological clogging in a two-dimentsional sandbox experiment

    DEFF Research Database (Denmark)

    Kildsgaard, J.; Engesgaard, Peter Knudegaard

    2002-01-01

    A two-dimensional flow experiment on biological clogging was carried out by biostimulating a sandbox packed with sand inoculated with bacteria. Biostimulation. consisted of continuously injecting nutrients (acetate and nitrate). Clogging was visualized by frequently carrying out colored tracer...

  2. Biological Imaging Software Tools

    Science.gov (United States)

    Eliceiri, Kevin W.; Berthold, Michael R.; Goldberg, Ilya G.; Ibáñez, Luis; Manjunath, B.S.; Martone, Maryann E.; Murphy, Robert F.; Peng, Hanchuan; Plant, Anne L.; Roysam, Badrinath; Stuurman, Nico; Swedlow, Jason R.; Tomancak, Pavel; Carpenter, Anne E.

    2013-01-01

    Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis, and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the challenges in that domain, and the overall status of available software for bioimage informatics, focusing on open source options. PMID:22743775

  3. Semiconductor Nanocrystals for Biological Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Aihua; Gu, Weiwei; Larabell, Carolyn; Alivisatos, A. Paul

    2005-06-28

    Conventional organic fluorophores suffer from poor photo stability, narrow absorption spectra and broad emission feature. Semiconductor nanocrystals, on the other hand, are highly photo-stable with broad absorption spectra and narrow size-tunable emission spectra. Recent advances in the synthesis of these materials have resulted in bright, sensitive, extremely photo-stable and biocompatible semiconductor fluorophores. Commercial availability facilitates their application in a variety of unprecedented biological experiments, including multiplexed cellular imaging, long-term in vitro and in vivo labeling, deep tissue structure mapping and single particle investigation of dynamic cellular processes. Semiconductor nanocrystals are one of the first examples of nanotechnology enabling a new class of biomedical applications.

  4. Experimenting with Mathematical Biology

    Science.gov (United States)

    Sanft, Rebecca; Walter, Anne

    2016-01-01

    St. Olaf College recently added a Mathematical Biology concentration to its curriculum. The core course, Mathematics of Biology, was redesigned to include a wet laboratory. The lab classes required students to collect data and implement the essential modeling techniques of formulation, implementation, validation, and analysis. The four labs…

  5. Image processing and recognition for biological images.

    Science.gov (United States)

    Uchida, Seiichi

    2013-05-01

    This paper reviews image processing and pattern recognition techniques, which will be useful to analyze bioimages. Although this paper does not provide their technical details, it will be possible to grasp their main tasks and typical tools to handle the tasks. Image processing is a large research area to improve the visibility of an input image and acquire some valuable information from it. As the main tasks of image processing, this paper introduces gray-level transformation, binarization, image filtering, image segmentation, visual object tracking, optical flow and image registration. Image pattern recognition is the technique to classify an input image into one of the predefined classes and also has a large research area. This paper overviews its two main modules, that is, feature extraction module and classification module. Throughout the paper, it will be emphasized that bioimage is a very difficult target for even state-of-the-art image processing and pattern recognition techniques due to noises, deformations, etc. This paper is expected to be one tutorial guide to bridge biology and image processing researchers for their further collaboration to tackle such a difficult target.

  6. [Biological experiments on "Kosmos-1887"].

    Science.gov (United States)

    Alpatov, A M; I'lin, E A; Antipov, V V; Tairbekov, M G

    1989-01-01

    In the 13-ray space flight on Kosmos-1887 various experiments in the field of cell biology, genetics, biorhythm, developmental biology and regeneration were performed using bacteria, protozoa, plants, worms, insects, fish and amphibia. Paramecia showed enhanced cell proliferation, spheroidization and diminished protein content. Experiments on fruit-flies, newt oocytes and primate lymphocytes confirmed involvement of the cell genetic apparatus in responses to microgravity. Beetles exhibited a reduction of the length of the spontaneous period of freely running circadian rhythms. Carausius morosus developed latent changes in early embryogenesis which manifested at later stages of ontogenesis. Exposure to microgravity did not prevent recovery of injured tissues; moreover their regeneration may be accelerated after recovery. Biology research programs in future biosatellite flights are discussed.

  7. Biological Imaging Capability in the ABRS Facility on ISS

    Science.gov (United States)

    Cox, David R.; Murdoch, T.; Regan, M. F.; Meshlberger, R. J.; Mortenson, T. E.; Albino, S. A.; Paul, A. L.; Ferl, R. J.

    2010-01-01

    This slide presentation reviews the Advanced Biological Research System (ABRS) on the International Space Station (ISS) and its biological imaging capability. The ABRS is an environmental control chamber. It has two indpendently controlled Experiment Research Chambers (ERCs) with temperature, relative humidity and carbon dioxide controls. ABRS is a third generation plant growth system. Several experiments are reviewed, with particular interest in the use of Green Fluorescent Protein (GFP) a non-destructive plant stress reporting mechanism, naturally found in jellyfish.

  8. Image processing and computing in structural biology

    NARCIS (Netherlands)

    Jiang, Linhua

    2009-01-01

    With the help of modern techniques of imaging processing and computing, image data obtained by electron cryo-microscopy of biomolecules can be reconstructed to three-dimensional biological models at sub-nanometer resolution. These models allow answering urgent problems in life science, for instance,

  9. Pushing the Envelope in Biological Imaging

    Science.gov (United States)

    Betzig, Eric

    2010-03-01

    Optical microscopy has been instrumental in studies of the structure and function of biological systems for centuries. However, many questions at the forefront of molecular, cellular, and neurobiology remain beyond its current capabilities. I will discuss efforts in my group to extend these capabilities in areas such as superresolution optics, photodamage mediation, high speed volumetric imaging, and deep tissue imaging.

  10. Porphyrin-magnetite nanoconjugates for biological imaging

    LENUS (Irish Health Repository)

    Nowostawska, Malgorzata

    2011-04-08

    Abstract Background The use of silica coated magnetic nanoparticles as contrast agents has resulted in the production of highly stable, non-toxic solutions that can be manipulated via an external magnetic field. As a result, the interaction of these nanocomposites with cells is of vital importance in understanding their behaviour and biocompatibility. Here we report the preparation, characterisation and potential application of new "two-in-one" magnetic fluorescent nanocomposites composed of silica-coated magnetite nanoparticles covalently linked to a porphyrin moiety. Method The experiments were performed by administering porphyrin functionalised silica-coated magnetite nanoparticles to THP-1 cells, a human acute monocytic leukaemia cell line. Cells were cultured in RPMI 1640 medium with 25 mM HEPES supplemented with heat-inactivated foetal bovine serum (FBS). Results We have synthesised, characterised and analysed in vitro, a new multimodal (magnetic and fluorescent) porphyrin magnetic nanoparticle composite (PMNC). Initial co-incubation experiments performed with THP-1 macrophage cells were promising; however the PMNC photobleached under confocal microscopy study. β-mercaptoethanol (β-ME) was employed to counteract this problem and resulted not only in enhanced fluorescence emission, but also allowed for elongated imaging and increased exposure times of the PMNC in a cellular environment. Conclusion Our experiments have demonstrated that β-ME visibly enhances the emission intensity. No deleterious effects to the cells were witnessed upon co-incubation with β-ME alone and no increases in background fluorescence were recorded. These results should present an interest for further development of in vitro biological imaging techniques.

  11. Nonlinear spectral imaging of biological tissues

    Science.gov (United States)

    Palero, J. A.

    2007-07-01

    The work presented in this thesis demonstrates live high resolution 3D imaging of tissue in its native state and environment. The nonlinear interaction between focussed femtosecond light pulses and the biological tissue results in the emission of natural autofluorescence and second-harmonic signal. Because biological intrinsic emission is generally very weak and extends from the ultraviolet to the visible spectral range, a broad-spectral range and high sensitivity 3D spectral imaging system is developed. Imaging the spectral characteristics of the biological intrinsic emission reveals the structure and biochemistry of the cells and extra-cellular components. By using different methods in visualizing the spectral images, discrimination between different tissue structures is achieved without the use of any stain or fluorescent label. For instance, RGB real color spectral images of the intrinsic emission of mouse skin tissues show blue cells, green hair follicles, and purple collagen fibers. The color signature of each tissue component is directly related to its characteristic emission spectrum. The results of this study show that skin tissue nonlinear intrinsic emission is mainly due to the autofluorescence of reduced nicotinamide adenine dinucleotide (phosphate), flavins, keratin, melanin, phospholipids, elastin and collagen and nonlinear Raman scattering and second-harmonic generation in Type I collagen. In vivo time-lapse spectral imaging is implemented to study metabolic changes in epidermal cells in tissues. Optical scattering in tissues, a key factor in determining the maximum achievable imaging depth, is also investigated in this work.

  12. Voyager imaging experiment

    Science.gov (United States)

    Smith, B.A.; Briggs, G.A.; Danielson, G.E.; Cook, A.F.; Davies, M.E.; Hunt, G.E.; Masursky, H.; Soderblom, L.A.; Owen, T.C.; Sagan, C.; Suomi, V.E.

    1977-01-01

    The overall objective of this experiment is exploratory reconnaissance of Jupiter, Saturn, their satellites, and Saturn's rings. Such reconnaissance, at resolutions and phase angles unobtainable from Earth, can be expected to provide much new data relevant to the atmospheric and/or surface properties of these bodies. The experiment also has the following specific objectives: Observe and characterize the global circulation of the atmospheres of Jupiter and Saturn; Determine the horizontal and vertical structure of the visible clouds and establish their relationship to the belted appearance and dynamical properties of the planetary atmospheres; Determine the vertical structure of high, optically-thin, scattering layers on Jupiter and Saturn; Determine the nature of anomalous features such as the Great Red Spot, South Equatorial Belt disturbances, etc.; Characterize the nature of the colored material in the clouds of Jupiter and Saturn, and identify the nature and sources of chromophores on Io and Titan; Perform comparative geologic studies of many satellites at less than 15-km resolution; Map and characterize the geologic structure of several satellites at high resolution (???1 km); Investigate the existence and nature of atmospheres on the satellites; Determine the mass, size, and shape of many of the satellites by direct measurement; Determine the direction of the spin axes and periods of rotation of several satellites, and establish coordinate systems for the larger satellites; Map the radial distribution of material in Saturn's rings at high resolution; Determine the optical scattering properties of the primaries, rings, and satellites at several wavelengths and phase angles; Search for novel physical phenomena, e.g., phenomena associated with the Io flux tube, meteors, aurorae, lightning, or satellite shadows. ?? 1977 D. Reidel Publishing Company.

  13. Imaging cellular and molecular biological functions

    Energy Technology Data Exchange (ETDEWEB)

    Shorte, S.L. [Institut Pasteur, 75 - Paris (France). Plateforme d' Imagerie Dynamique PFID-Imagopole; Frischknecht, F. (eds.) [Heidelberg Univ. Medical School (Germany). Dept. of Parasitology

    2007-07-01

    'Imaging cellular and molecular biological function' provides a unique selection of essays by leading experts, aiming at scientist and student alike who are interested in all aspects of modern imaging, from its application and up-scaling to its development. Indeed the philosophy of this volume is to provide student, researcher, PI, professional or provost the means to enter this applications field with confidence, and to construct the means to answer their own specific questions. (orig.)

  14. microlith : Image Simulation for Biological Phase Microscopy

    CERN Document Server

    Mehta, Shalin B

    2013-01-01

    Accurate simulation of image formation remains under-exploited for biological phase microscopy methods that employ partially coherent illumination, despite being important for the design of imaging systems and the reconstruction algorithms. We present an open-source MATLAB toolbox, microlith (https://code.google.com/p/microlith), that provides accurate simulation of the 3D image of a thin specimen under any partially coherent imaging system, including coherent or incoherent systems. We demonstrate the accuracy of the microlith toolbox by comparing simulated images and experimental images of a phase-only Siemens star test target using dark field and differential interference contrast microscopes. The comparison leads to intriguing insights about the sensitivity of the dark-field microscope to sub-resolution features and effects of specimen birefringence on differential interference contrast.

  15. Portable Imaging Polarimeter and Imaging Experiments

    Energy Technology Data Exchange (ETDEWEB)

    PHIPPS,GARY S.; KEMME,SHANALYN A.; SWEATT,WILLIAM C.; DESCOUR,M.R.; GARCIA,J.P.; DERENIAK,E.L.

    1999-11-01

    Polarimetry is the method of recording the state of polarization of light. Imaging polarimetry extends this method to recording the spatially resolved state of polarization within a scene. Imaging-polarimetry data have the potential to improve the detection of manmade objects in natural backgrounds. We have constructed a midwave infrared complete imaging polarimeter consisting of a fixed wire-grid polarizer and rotating form-birefringent retarder. The retardance and the orientation angles of the retarder were optimized to minimize the sensitivity of the instrument to noise in the measurements. The optimal retardance was found to be 132{degree} rather than the typical 90{degree}. The complete imaging polarimeter utilized a liquid-nitrogen cooled PtSi camera. The fixed wire-grid polarizer was located at the cold stop inside the camera dewar. The complete imaging polarimeter was operated in the 4.42-5 {micro}m spectral range. A series of imaging experiments was performed using as targets a surface of water, an automobile, and an aircraft. Further analysis of the polarization measurements revealed that in all three cases the magnitude of circular polarization was comparable to the noise in the calculated Stokes-vector components.

  16. Pattern recognition software and techniques for biological image analysis.

    Directory of Open Access Journals (Sweden)

    Lior Shamir

    Full Text Available The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays.

  17. Pattern recognition software and techniques for biological image analysis.

    Science.gov (United States)

    Shamir, Lior; Delaney, John D; Orlov, Nikita; Eckley, D Mark; Goldberg, Ilya G

    2010-11-24

    The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays.

  18. Nonlinear spectral imaging of biological tissues

    NARCIS (Netherlands)

    Palero, J.A.

    2007-01-01

    The work presented in this thesis demonstrates live high resolution 3D imaging of tissue in its native state and environment. The nonlinear interaction between focussed femtosecond light pulses and the biological tissue results in the emission of natural autofluorescence and second-harmonic signal.

  19. Nonlinear spectral imaging of biological tissues

    NARCIS (Netherlands)

    Palero, J.A.

    2007-01-01

    The work presented in this thesis demonstrates live high resolution 3D imaging of tissue in its native state and environment. The nonlinear interaction between focussed femtosecond light pulses and the biological tissue results in the emission of natural autofluorescence and second-harmonic signal.

  20. X-ray Absorption Spectroscopy and Coherent X-ray Diffraction Imaging for Time-Resolved Investigation of the Biological Complexes: Computer Modelling towards the XFEL Experiment

    Science.gov (United States)

    Bugaev, A. L.; Guda, A. A.; Yefanov, O. M.; Lorenz, U.; Soldatov, A. V.; Vartanyants, I. A.

    2016-05-01

    The development of the next generation synchrotron radiation sources - free electron lasers - is approaching to become an effective tool for the time-resolved experiments aimed to solve actual problems in various fields such as chemistry’ biology’ medicine’ etc. In order to demonstrate’ how these experiments may be performed for the real systems to obtain information at the atomic and macromolecular levels’ we have performed a molecular dynamics computer simulation combined with quantum chemistry calculations for the human phosphoglycerate kinase enzyme with Mg containing substrate. The simulated structures were used to calculate coherent X-ray diffraction patterns’ reflecting the conformational state of the enzyme, and Mg K-edge X-ray absorption spectra, which depend on the local structure of the substrate. These two techniques give complementary information making such an approach highly effective for time-resolved investigation of various biological complexes, such as metalloproteins or enzymes with metal-containing substrate, to obtain information about both metal-containing active site or substrate and the atomic structure of each conformation.

  1. Biological experiments - The Viking Mars Lander.

    Science.gov (United States)

    Klein, H. P.; Lederberg, J.; Rich, A.

    1972-01-01

    From the biological point of view, the Viking 1975 mission might be regarded as a test of the Oparin-Haldane hypothesis concerning the chemical evolution of living systems. Mars is a planet whose early history was probably similar to that of the earth and whose present environmental conditions may be compatible with the maintenance of living organisms. Thus, the biological experiments aboard the Viking I spacecraft are primarily concerned with the question of whether chemical evolution on Mars took place, and, if so, whether the process reached a level of complexity characteristic of replicating systems.

  2. Bodily experiences in secondary school biology

    Science.gov (United States)

    Orlander, Auli Arvola; Wickman, Per-Olof

    2011-09-01

    This is a study of teaching about the human body. It is based on transcribed material from interviews with 15-year-old students and teachers about their experiences of sex education and from recordings of classroom interactions during a dissection. The analysis is focused on the relationship between what students are supposed to learn about the biological body and their expressed experiences and meaning making of bodies in the schoolwork. The results indicate that the negotiations associated with the encounters between the bodies of the classroom (student, teacher, and animal bodies) are important for what directions meaning making takes and what students are afforded to learn about bodies, biologically as well as in terms of values. We suggest that these negotiations should be taken into account at schools, be regarded as an important part of the learning processes in science education and in that way open up for new possibilities for students' meaning making.

  3. Imaging morphogenesis: technological advances and biological insights.

    Science.gov (United States)

    Keller, Philipp J

    2013-06-01

    Morphogenesis, the development of the shape of an organism, is a dynamic process on a multitude of scales, from fast subcellular rearrangements and cell movements to slow structural changes at the whole-organism level. Live-imaging approaches based on light microscopy reveal the intricate dynamics of this process and are thus indispensable for investigating the underlying mechanisms. This Review discusses emerging imaging techniques that can record morphogenesis at temporal scales from seconds to days and at spatial scales from hundreds of nanometers to several millimeters. To unlock their full potential, these methods need to be matched with new computational approaches and physical models that help convert highly complex image data sets into biological insights.

  4. Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

    Science.gov (United States)

    Gilad, Assaf A; Shapiro, Mikhail G

    2017-06-01

    Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

  5. Probing bacterial cell biology using image cytometry.

    Science.gov (United States)

    Cass, Julie A; Stylianidou, Stella; Kuwada, Nathan J; Traxler, Beth; Wiggins, Paul A

    2017-03-01

    Advances in automated fluorescence microscopy have made snapshot and time-lapse imaging of bacterial cells commonplace, yet fundamental challenges remain in analysis. The vast quantity of data collected in high-throughput experiments requires a fast and reliable automated method to analyze fluorescence intensity and localization, cell morphology and proliferation as well as other descriptors. Inspired by effective yet tractable methods of population-level analysis using flow cytometry, we have developed a framework and tools for facilitating analogous analyses in image cytometry. These tools can both visualize and gate (generate subpopulations) more than 70 cell descriptors, including cell size, age and fluorescence. The method is well suited to multi-well imaging, analysis of bacterial cultures with high cell density (thousands of cells per frame) and complete cell cycle imaging. We give a brief description of the analysis of four distinct applications to emphasize the broad applicability of the tool.

  6. Cell biology experiments conducted in space

    Science.gov (United States)

    Taylor, G. R.

    1977-01-01

    A review of cell biology experiments conducted during the first two decades of space flight is provided. References are tabulated for work done with six types of living test system: isolated viruses, bacteriophage-host, bacteria, yeasts and filamentous fungi, protozoans, and small groups of cells (such as hamster cell tissue and fertilized frog eggs). The general results of studies involving the survival of cells in space, the effect of space flight on growing cultures, the biological effects of multicharged high-energy particles, and the effects of space flight on the genetic apparatus of microorganisms are summarized. It is concluded that cell systems remain sufficiently stable during space flight to permit experimentation with models requiring a fixed cell line during the space shuttle era.

  7. Cell biology experiments conducted in space

    Science.gov (United States)

    Taylor, G. R.

    1977-01-01

    A review of cell biology experiments conducted during the first two decades of space flight is provided. References are tabulated for work done with six types of living test system: isolated viruses, bacteriophage-host, bacteria, yeasts and filamentous fungi, protozoans, and small groups of cells (such as hamster cell tissue and fertilized frog eggs). The general results of studies involving the survival of cells in space, the effect of space flight on growing cultures, the biological effects of multicharged high-energy particles, and the effects of space flight on the genetic apparatus of microorganisms are summarized. It is concluded that cell systems remain sufficiently stable during space flight to permit experimentation with models requiring a fixed cell line during the space shuttle era.

  8. Application of Quantum Dots in Biological Imaging

    Directory of Open Access Journals (Sweden)

    Shan Jin

    2011-01-01

    Full Text Available Quantum dots (QDs are a group of semiconducting nanomaterials with unique optical and electronic properties. They have distinct advantages over traditional fluorescent organic dyes in chemical and biological studies in terms of tunable emission spectra, signal brightness, photostability, and so forth. Currently, the major type of QDs is the heavy metal-containing II-IV, IV-VI, or III-V QDs. Silicon QDs and conjugated polymer dots have also been developed in order to lower the potential toxicity of the fluorescent probes for biological applications. Aqueous solubility is the common problem for all types of QDs when they are employed in the biological researches, such as in vitro and in vivo imaging. To circumvent this problem, ligand exchange and polymer coating are proven to be effective, besides synthesizing QDs in aqueous solutions directly. However, toxicity is another big concern especially for in vivo studies. Ligand protection and core/shell structure can partly solve this problem. With the rapid development of QDs research, new elements and new morphologies have been introduced to this area to fabricate more safe and efficient QDs for biological applications.

  9. U.S. biological experiments in space

    Science.gov (United States)

    Klein, H. P.

    1981-01-01

    The history of biologic experimentation in space is traced. Early balloon and rocket borne animals showed no abnormalities on the macroscale, and biosatellite launches with bacteria and amoebae revealed no microscopic dysfunctions. Adult Drosophila flies on board Cosmos spacecraft died with a shortened lifespan, while their offspring lived full lifespans. Green pepper plants grown in weightlessness showed a different orientation, but no physiological disturbances. Normal bone growth in rats has been found to almost cease after 11 days in space, and the mean life span of red blood cells decreases by four days. A series of experiments designed by U.S. scientists will be performed on primates provided and flown by the U.S.S.R. Finally, experiments on board Spacelab will involve determination of the persistence of circadian rhythms in bacteria and humans.

  10. U.S. biological experiments in space

    Science.gov (United States)

    Klein, H. P.

    1981-01-01

    The history of biologic experimentation in space is traced. Early balloon and rocket borne animals showed no abnormalities on the macroscale, and biosatellite launches with bacteria and amoebae revealed no microscopic dysfunctions. Adult Drosophila flies on board Cosmos spacecraft died with a shortened lifespan, while their offspring lived full lifespans. Green pepper plants grown in weightlessness showed a different orientation, but no physiological disturbances. Normal bone growth in rats has been found to almost cease after 11 days in space, and the mean life span of red blood cells decreases by four days. A series of experiments designed by U.S. scientists will be performed on primates provided and flown by the U.S.S.R. Finally, experiments on board Spacelab will involve determination of the persistence of circadian rhythms in bacteria and humans.

  11. Fluorescence confocal endomicroscopy in biological imaging

    Science.gov (United States)

    Delaney, Peter; Thomas, Steven; Allen, John; McLaren, Wendy; Murr, Elise; Harris, Martin

    2007-02-01

    In vivo fluorescence microscopic imaging of biological systems in human disease states and animal models is possible with high optical resolution and mega pixel point-scanning performance using optimised off-the-shelf turn-key devices. There are however various trade-offs between tissue access and instrument performance when miniaturising in vivo microscopy systems. A miniature confocal scanning technology that was developed for clinical human endoscopy has been configured into a portable device for direct hand-held interrogation of living tissue in whole animal models (Optiscan FIVE-1 system). Scanning probes of 6.3mm diameter with a distal tip diameter of 5.0mm were constructed either in a 150mm length for accessible tissue, or a 300mm probe for laparoscopic interrogation of internal tissues in larger animal models. Both devices collect fluorescence confocal images (excitation 488 nm; emission >505 or >550 nm) comprised of 1024 x 1204 sampling points/image frame, with lateral resolution 0.7um; axial resolution 7um; FOV 475 x 475um. The operator can dynamically control imaging depth from the tissue surface to approx 250um in 4um steps via an internally integrated zaxis actuator. Further miniaturisation is achieved using an imaging contact probe based on scanning the proximal end of a high-density optical fibre bundle (~30,000 fibres) of sheep and pigs was fluorescently stained with calcein-AM or fluorescein. Surface and sub-surface cellular and sub-cellular details could be readily visualised in vivo at high resolution. In rodent disease models, in vivo endomicroscopy with appropriate fluorescent agents allowed examination of thrombosis formation, tumour microvasculature and liver metastases, diagnosis and staging of ulcerative colitis, liver necrosis and glomerulonephritis. Miniaturised confocal endomicroscopy allows rapid in vivo molecular and subsurface microscopy of normal and pathologic tissue at high resolution in small and large whole animal models

  12. Destination visual image and expectation of experiences

    DEFF Research Database (Denmark)

    Ye, H.; Tussyadiah, Iis

    2011-01-01

    at understanding how a visual image is relevant to the expectation of experiences by deconstructing images of a destination and interpreting visitors' perceptions of these images and the experiences associated with them. The results suggest that tourists with different understandings of desirable experiences found...

  13. Radionuclide Imaging Technologies for Biological Systems

    Energy Technology Data Exchange (ETDEWEB)

    Howell, Calvin R. [Duke Univ., Durham, NC (United States); Reid, Chantal D. [Duke Univ., Durham, NC (United States); Weisenberger, Andrew G. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States)

    2014-05-14

    The main objective of this project is to develop technologies and experimental techniques for studying the dynamics of physiological responses of plants to changes in their interface with the local environment and to educate a new generation of scientists in an interdisciplinary environment of biology, physics and engineering. Also an important goal is to perform measurements to demonstrate the new data that can be produced and made available to the plant-biology community using the imaging technologies and experimental techniques developed in this project. The study of the plant-environment interface includes a wide range of topics in plant physiology, e.g., the root-soil interface, resource availability, impact of herbivores, influence of microbes on root surface, and responses to toxins in the air and soil. The initial scientific motivation for our work is to improve understanding of the mechanisms for physiological responses to abrupt changes in the local environment, in particular, the responses that result in short-term adjustments in resource (e.g., sugars, nutrients and water) allocations. Data of time-dependent responses of plants to environmental changes are essential in developing mechanistic models for substance intake and resource allocation. Our approach is to use radioisotope tracing techniques to study whole-plant and plant organ (e.g., leaves, stems, roots) dynamical responses to abrupt changes in environmental conditions such as concentration of CO2 in the atmosphere, nutrient availability and lighting. To this aim we are collaborating with the Radiation Detector and Imaging Group at the Thomas Jefferson National Laboratory Facility (JLab) to develop gamma-ray and beta particle imaging systems optimized for plant studies. The radioisotope tracing measurements are conducted at the Phytotron facility at Duke University. The Phytotron is a controlled environment plant research facility with a variety of plant growth chambers. One chamber

  14. A review of imaging techniques for systems biology

    Directory of Open Access Journals (Sweden)

    Po Ming J

    2008-08-01

    Full Text Available Abstract This paper presents a review of imaging techniques and of their utility in system biology. During the last decade systems biology has matured into a distinct field and imaging has been increasingly used to enable the interplay of experimental and theoretical biology. In this review, we describe and compare the roles of microscopy, ultrasound, CT (Computed Tomography, MRI (Magnetic Resonance Imaging, PET (Positron Emission Tomography, and molecular probes such as quantum dots and nanoshells in systems biology. As a unified application area among these different imaging techniques, examples in cancer targeting are highlighted.

  15. A Biologically Inspired CMOS Image Sensor

    CERN Document Server

    Sarkar, Mukul

    2013-01-01

    Biological systems are a source of inspiration in the development of small autonomous sensor nodes. The two major types of optical vision systems found in nature are the single aperture human eye and the compound eye of insects. The latter are among the most compact and smallest vision sensors. The eye is a compound of individual lenses with their own photoreceptor arrays.  The visual system of insects allows them to fly with a limited intelligence and brain processing power. A CMOS image sensor replicating the perception of vision in insects is discussed and designed in this book for industrial (machine vision) and medical applications. The CMOS metal layer is used to create an embedded micro-polarizer able to sense polarization information. This polarization information is shown to be useful in applications like real time material classification and autonomous agent navigation. Further the sensor is equipped with in pixel analog and digital memories which allow variation of the dynamic range and in-pixel b...

  16. FY05 LDRD Final Report, A Revolution in Biological Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, H N; Bajt, S; Balhorn, R; Barty, A; Barsky, D; Bogan, M; Chung, S; Frank, M; Hau-Riege, S; Ishii, H; London, R; Marchesini, S; Noy, A; Segelke, B; Szoke, A; Szoke, H; Trebes, J; Wootton, A; Hajdu, J; Bergh, M; Caleman, C; Huldt, G; Lejon, S; der Spoel, D v; Howells, M; He, H; Spence, J; Nugent, K; Ingerman, E

    2006-01-20

    X-ray free-electron lasers (XFELs) are currently under development and will provide a peak brightness more than 10 orders of magnitude higher than modern synchrotrons. The goal of this project was to perform the fundamental research to evaluate the possibility of harnessing these unique x-ray sources to image single biological particles and molecules at atomic resolution. Using a combination of computational modeling and experimental verification where possible, they showed that it should indeed be possible to record coherent scattering patterns from single molecules with pulses that are shorter than the timescales for the degradation of the structure due to the interaction with those pulses. They used these models to determine the effectiveness of strategies to allow imaging using longer XFEL pulses and to design validation experiments to be carried out at interim ultrafast sources. They also developed and demonstrated methods to recover three-dimensional (3D) images from coherent diffraction patterns, similar to those expected from XFELs. The images of micron-sized test objects are the highest-resolution 3D images of any noncrystalline material ever formed with x-rays. The project resulted in 14 publications in peer-reviewed journals and four records of invention.

  17. Biological imaging with coherent Raman scattering microscopy: a tutorial

    Science.gov (United States)

    Alfonso-García, Alba; Mittal, Richa; Lee, Eun Seong; Potma, Eric O.

    2014-01-01

    Abstract. Coherent Raman scattering (CRS) microscopy is gaining acceptance as a valuable addition to the imaging toolset of biological researchers. Optimal use of this label-free imaging technique benefits from a basic understanding of the physical principles and technical merits of the CRS microscope. This tutorial offers qualitative explanations of the principles behind CRS microscopy and provides information about the applicability of this nonlinear optical imaging approach for biological research. PMID:24615671

  18. Patient Preference for Dosing Frequency Based on Prior Biologic Experience.

    Science.gov (United States)

    Zhang, Mingliang; Carter, Chureen; Olson, William H; Johnson, Michael P; Brennem, Susan K; Lee, Seina; Farahi, Kamyar

    2017-03-01

    There is limited research exploring patient preferences regarding dosing frequency of biologic treatment of psoriasis. Patients with moderate-to-severe plaque psoriasis identified in a healthcare claims database completed a survey regarding experience with psoriasis treatments and preferred dosing frequency. Survey questions regarding preferences were posed in two ways: (1) by likelihood of choosing once per week or 2 weeks, or 12 weeks; and (2) by choosing one option among once every 1-2 or 3-4 weeks or 1-2 or 2-3 months. Data were analyzed by prior biologic history (biologic-experienced vs biologic-naïve, and with one or two specific biologics). Overall, 426 patients completed the survey: 163 biologic-naïve patients and 263 biologic-experienced patients (159 had some experience with etanercept, 105 with adalimumab, and 49 with ustekinumab). Among patients who indicated experience with one or two biologics, data were available for 219 (30 with three biologics and 14 did not specify which biologic experience). The majority of biologic-naïve (68.8%) and overall biologic-experienced (69.4%) patients indicated that they were very likely to choose the least frequent dosing option of once every 12 weeks (Table 1). In contrast, fewer biologic-naïve (9.1% and 16.7%) and biologic-experienced (22.5% and 25.3%) patients indicated that they were very likely to choose the 1-week and 2-week dosing interval options, respectively. In each cohort grouped by experience with specific biologics, among those with no experience with ustekinumab, the most chosen option was 1-2 weeks. The most frequently chosen option was every 2-3 months, among patients with any experience with ustekinumab, regardless of their experience with other biologics. The least frequent dosing interval was preferred among biologic naïve patients and patients who had any experience with ustekinumab. Dosing interval may influence the shared decision-making process for psoriasis treatment with biologics. J

  19. A physicist at Woods Hole: introducing the image intensifier and image processing to cell biology.

    Science.gov (United States)

    Anderson, Nancy

    2010-09-01

    In 1963, by invitation, particle physicist George Reynolds (Princeton University) brought an image intensifier to Woods Hole Marine Biological Laboratory. Together, he and a group of biologists began experimenting with the device as a way to create images of cells in low-light level situations, especially in the study of bioluminescence. In this paper I am interested in how the scientists, a physicist and biologists in collaboration, assessed, interpreted and presented the pictures that they created with the aid of image intensification. In particular, I consider the problem of 'noise' in the image. The paper ends with an example of how Reynolds and a biologist at Woods Hole contended with the presence of noise in images used for publication. Here is an example of how data is modified, that is, enhanced, to serve as scientific evidence. By presenting an early and simple case of the altered image I reveal one way scientists addressed the potentiality of presenting inappropriately modified data - a concern that has garnered much attention in the current age of digital imaging technologies. (c) 2010 Elsevier Ltd. All rights reserved.

  20. The Galileo Solid-State Imaging experiment

    Science.gov (United States)

    Belton, Michael J. S.; Klaasen, Kenneth P.; Clary, Maurice C.; Anderson, James L.; Anger, Clifford D.; Carr, Michael H.; Chapman, Clark R.; Davies, Merton E.; Greeley, Ronald; Anderson, Donald

    1992-01-01

    The Galileo Orbiter's Solid-State Imaging (SSI) experiment uses a 1.5-m focal length TV camera with 800 x 800 pixel, virtual-phase CCD detector in order to obtain images of Jupiter and its satellites which possess a combination of sensitivity levels, spatial resolutions, geometric fidelity, and spectral range that are unmatched by earlier imaging data. After describing the performance of this equipment on the basis of ground calibrations, attention is given to the SSI experiment's Jupiter system observation objectives; these encompass atmospheric science, satellite surfaces, ring structure, and 'darkside' experiments.

  1. Rotating biological contactors: the Canadian experience

    Energy Technology Data Exchange (ETDEWEB)

    Cuenca, Manuel A. [Ryerson Polytechnical Univ., Toronto, ON (Canada). Chemical Engineering Dept.; Smith, Tom [CMS Rotordisk Inc., Concord, ON (Canada); Vianna, Arlinda C. [Servico Nacional de Aprendizagem Industrial (SENAI), Salvador, BA (Brazil)

    1993-12-31

    In fifteen years, Rotating Biological Contactors (RBC) have become one of the most attractive technologies for secondary wastewater treatment. The present work is a review of the evolution of RBC technology in the last twenty years. In addition, the status of the technology in Canada is described, emphasizing industrial facilities and landfill leachate treatment. An enumeration of the most relevant development areas is included. (author). 34 refs., 3 figs., 7 tabs.

  2. Automated force volume image processing for biological samples.

    Directory of Open Access Journals (Sweden)

    Pavel Polyakov

    Full Text Available Atomic force microscopy (AFM has now become a powerful technique for investigating on a molecular level, surface forces, nanomechanical properties of deformable particles, biomolecular interactions, kinetics, and dynamic processes. This paper specifically focuses on the analysis of AFM force curves collected on biological systems, in particular, bacteria. The goal is to provide fully automated tools to achieve theoretical interpretation of force curves on the basis of adequate, available physical models. In this respect, we propose two algorithms, one for the processing of approach force curves and another for the quantitative analysis of retraction force curves. In the former, electrostatic interactions prior to contact between AFM probe and bacterium are accounted for and mechanical interactions operating after contact are described in terms of Hertz-Hooke formalism. Retraction force curves are analyzed on the basis of the Freely Jointed Chain model. For both algorithms, the quantitative reconstruction of force curves is based on the robust detection of critical points (jumps, changes of slope or changes of curvature which mark the transitions between the various relevant interactions taking place between the AFM tip and the studied sample during approach and retraction. Once the key regions of separation distance and indentation are detected, the physical parameters describing the relevant interactions operating in these regions are extracted making use of regression procedure for fitting experiments to theory. The flexibility, accuracy and strength of the algorithms are illustrated with the processing of two force-volume images, which collect a large set of approach and retraction curves measured on a single biological surface. For each force-volume image, several maps are generated, representing the spatial distribution of the searched physical parameters as estimated for each pixel of the force-volume image.

  3. Automated Force Volume Image Processing for Biological Samples

    Science.gov (United States)

    Duan, Junbo; Duval, Jérôme F. L.; Brie, David; Francius, Grégory

    2011-01-01

    Atomic force microscopy (AFM) has now become a powerful technique for investigating on a molecular level, surface forces, nanomechanical properties of deformable particles, biomolecular interactions, kinetics, and dynamic processes. This paper specifically focuses on the analysis of AFM force curves collected on biological systems, in particular, bacteria. The goal is to provide fully automated tools to achieve theoretical interpretation of force curves on the basis of adequate, available physical models. In this respect, we propose two algorithms, one for the processing of approach force curves and another for the quantitative analysis of retraction force curves. In the former, electrostatic interactions prior to contact between AFM probe and bacterium are accounted for and mechanical interactions operating after contact are described in terms of Hertz-Hooke formalism. Retraction force curves are analyzed on the basis of the Freely Jointed Chain model. For both algorithms, the quantitative reconstruction of force curves is based on the robust detection of critical points (jumps, changes of slope or changes of curvature) which mark the transitions between the various relevant interactions taking place between the AFM tip and the studied sample during approach and retraction. Once the key regions of separation distance and indentation are detected, the physical parameters describing the relevant interactions operating in these regions are extracted making use of regression procedure for fitting experiments to theory. The flexibility, accuracy and strength of the algorithms are illustrated with the processing of two force-volume images, which collect a large set of approach and retraction curves measured on a single biological surface. For each force-volume image, several maps are generated, representing the spatial distribution of the searched physical parameters as estimated for each pixel of the force-volume image. PMID:21559483

  4. Morphogenesis and pattern formation in biological systems experiments and models

    CERN Document Server

    Noji, Sumihare; Ueno, Naoto; Maini, Philip

    2003-01-01

    A central goal of current biology is to decode the mechanisms that underlie the processes of morphogenesis and pattern formation. Concerned with the analysis of those phenomena, this book covers a broad range of research fields, including developmental biology, molecular biology, plant morphogenesis, ecology, epidemiology, medicine, paleontology, evolutionary biology, mathematical biology, and computational biology. In Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, experimental and theoretical aspects of biology are integrated for the construction and investigation of models of complex processes. This collection of articles on the latest advances by leading researchers not only brings together work from a wide spectrum of disciplines, but also provides a stepping-stone to the creation of new areas of discovery.

  5. Biological effects of exposure to magnetic resonance imaging: an overview

    OpenAIRE

    Formica Domenico; Silvestri Sergio

    2004-01-01

    Abstract The literature on biological effects of magnetic and electromagnetic fields commonly utilized in magnetic resonance imaging systems is surveyed here. After an introduction on the basic principles of magnetic resonance imaging and the electric and magnetic properties of biological tissues, the basic phenomena to understand the bio-effects are described in classical terms. Values of field strengths and frequencies commonly utilized in these diagnostic systems are reported in order to a...

  6. Analyzing and mining automated imaging experiments.

    Science.gov (United States)

    Berlage, Thomas

    2007-04-01

    Image mining is the application of computer-based techniques that extract and exploit information from large image sets to support human users in generating knowledge from these sources. This review focuses on biomedical applications of this technique, in particular automated imaging at the cellular level. Due to increasing automation and the availability of integrated instruments, biomedical users are becoming increasingly confronted with the problem of analyzing such data. Image database applications need to combine data management, image analysis and visual data mining. The main point of such a system is a software layer that represents objects within an image and the ability to use a large spectrum of quantitative and symbolic object features. Image analysis needs to be adapted to each particular experiment; therefore, 'end user programming' will be desired to make the technology more widely applicable.

  7. A Biologically Inspired CMOS Image Sensor

    NARCIS (Netherlands)

    Sarkar, M.

    2011-01-01

    Biological systems are a source of inspiration in the development of small autonomous sensor nodes. The two major types of optical vision systems found in nature are the single aperture human eye and the compound eye of insects. The latter are among the most compact and smallest vision sensors. The

  8. Conjugate Meningococcal Vaccines Development: GSK Biologicals Experience

    Directory of Open Access Journals (Sweden)

    Jacqueline M. Miller

    2011-01-01

    Full Text Available Meningococcal diseases are serious threats to global health, and new vaccines specifically tailored to meet the age-related needs of various geographical areas are required. This paper focuses on the meningococcal conjugate vaccines developed by GSK Biologicals. Two combined conjugate vaccines were developed to help protect infants and young children in countries where the incidence of meningococcal serogroup C or serogroup C and Y disease is important: Hib-MenC-TT vaccine, which offers protection against Haemophilus influenzae type b and Neisseria meningitidis serogroup C diseases, is approved in several countries; and Hib-MenCY-TT vaccine, which adds N. meningitidis serogroup Y antigen, is currently in the final stages of development. Additionally, a tetravalent conjugate vaccine (MenACWY-TT designed to help protect against four meningococcal serogroups is presently being evaluated for global use in all age groups. All of these vaccines were shown to be highly immunogenic and to have clinically acceptable safety profiles.

  9. Partnerships Drive Informatics Solutions for Biological Imaging at Ocean Observatories

    Science.gov (United States)

    Sosik, H. M.; Futrelle, J.; Maffei, A. R.

    2012-12-01

    In the big-data, era informatics-oriented partnerships are needed to achieve improved scientific results and understanding. Our teams' experience shows that formal methodologies to build interdisciplinary partnerships enable us to efficiently produce needed technological innovation. One-on-one partnerships between individual research scientists and informaticists provide a crucial building block for supporting larger, nested partnerships. We present one such partnership as an example. As ocean observatories mature, they produce data at a pace that threatens to overwhelm the capacity of individual researchers to manage and analyze it. Our multi-disciplinary team has addressed these challenges in the context of a study involving very large numbers (~1 billion) of images collected by Imaging FlowCytobot, an automated submersible flow cytometer that continuously images plankton at up to 10hz. These data provide novel insights into coastal ecosystem dynamics, including characterization of biological responses to environmental change and early warning of harmful algal blooms. In contrast with the traditional focus on technology adoption, we have instead emphasized building partnerships between oceanographers and computer scientists. In these partnerships we identify use cases, design solutions, develop prototypes, and refine them until they meet oceanographers' science needs. In doing so we have found that rapid and significant advances do not always require technological innovations, but rather effective communication, focus on science outcomes, and an iterative design and evaluation process. In this work we have adopted a methodology developed in the Tetherless World Constellation at Rensselaer Polytechnic Institute, a framework that has been used for several data-intensive earth science applications. The prototype system produced for Imaging FlowCytobot data provides simple and ubiquitous access to observational data and products via web services and includes a data

  10. Embryonic stem cell biology: insights from molecular imaging.

    Science.gov (United States)

    Sallam, Karim; Wu, Joseph C

    2010-01-01

    Embryonic stem (ES) cells have therapeutic potential in disorders of cellular loss such as myocardial infarction, type I diabetes and neurodegenerative disorders. ES cell biology in living subjects was largely poorly understood until incorporation of molecular imaging into the field. Reporter gene imaging works by integrating a reporter gene into ES cells and using a reporter probe to induce a signal detectable by normal imaging modalities. Reporter gene imaging allows for longitudinal tracking of ES cells within the same host for a prolonged period of time. This has advantages over postmortem immunohistochemistry and traditional imaging modalities. The advantages include expression of reporter gene is limited to viable cells, expression is conserved between generations of dividing cells, and expression can be linked to a specific population of cells. These advantages were especially useful in studying a dynamic cell population such as ES cells and proved useful in elucidating the biology of ES cells. Reporter gene imaging identified poor integration of differentiated ES cells transplanted into host tissue as well as delayed donor cell death as reasons for poor long-term survival in vivo. This imaging technology also confirmed that ES cells indeed have immunogenic properties that factor into cell survival and differentiation. Finally, reporter gene imaging improved our understanding of the neoplastic risk of undifferentiated ES cells in forming teratomas. Despite such advances, much remains to be understood about ES cell biology to translate this technology to the bedside, and reporter gene imaging will certainly play a key role in formulating this understanding.

  11. A compact gamma camera for biological imaging

    Energy Technology Data Exchange (ETDEWEB)

    Bradley, E L; Cella, J; Majewski, S; Popov, V; Qian, Jianguo; Saha, M S; Smith, M F; Weisenberger, A G; Welsh, R E

    2006-02-01

    A compact detector, sized particularly for imaging a mouse, is described. The active area of the detector is approximately 46 mm; spl times/ 96 mm. Two flat-panel Hamamatsu H8500 position-sensitive photomultiplier tubes (PSPMTs) are coupled to a pixellated NaI(Tl) scintillator which views the animal through a copper-beryllium (CuBe) parallel-hole collimator specially designed for {sup 125}I. Although the PSPMTs have insensitive areas at their edges and there is a physical gap, corrections for scintillation light collection at the junction between the two tubes results in a uniform response across the entire rectangular area of the detector. The system described has been developed to optimize both sensitivity and resolution for in-vivo imaging of small animals injected with iodinated compounds. We demonstrate an in-vivo application of this detector, particularly to SPECT, by imaging mice injected with approximately 10-15; spl mu/Ci of {sup 125}I.

  12. Establishing laboratory standards for biological flight experiments

    Science.gov (United States)

    Young, Ronald B.; Moriarity, Debra M.

    1989-01-01

    The general objective of this research was to assess the effects of exposure to simulated microgravity on ultrastructural aspects of the contractile system in chicken skeletal muscle cells. This general objective had two specific experimental components: (1) the progression of changes in cell morphology, fusion, and patterns of contractile filament organization in muscle cell cultures grown in hollow fibers in the Clinostat were evaluated, with appropriate controls; (2) to initiate experiments in which muscle cells were grown on the surface of microcarrier beads. The ultimate objective of this second portion of the work is to determine if these beads can be rotated in a bioreactor and thereby obtain a more accurate approximation of the effects of simulated microgravity on differentiated muscle cells.

  13. Nucleic Acid--Based Nanodevices in Biological Imaging

    Science.gov (United States)

    Chakraborty, Kasturi; Veetil, Aneesh T.

    2017-01-01

    The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid--based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid--based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand. PMID:27294440

  14. Nucleic Acid-Based Nanodevices in Biological Imaging.

    Science.gov (United States)

    Chakraborty, Kasturi; Veetil, Aneesh T; Jaffrey, Samie R; Krishnan, Yamuna

    2016-06-02

    The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.

  15. THz imaging of majolica tiles and biological attached marble fragments

    Science.gov (United States)

    Catapano, Ilaria; Soldovieri, Francesco

    2016-04-01

    characterization of defects; - the imaging of layered structures and inner features. Specifically, as far as majolica tiles are concerned, we obtained cross-section images pointing out the presence of clay body, glaze and pigment layer. Moreover, pigment and glaze losses affecting the integrity of the surveyed objects were imaged, the depth extension of the losses was estimated and clay body inhomogeneities were observed. Finally, by taking into account the retrieved features of the topography and the spatial distribution of the detected clay body inhomogeneities, hypothesis on the clay shaping modalities were inferred. In addition, with reference to the marble fragment, the zones mainly affected by the biological attach were identified. A detailed presentation of the surveys and obtained results will be provided at the conferences. REFERENCES [1] W.L. Chan, J. Deibel, D.M. Mittleman, "Imaging with terahertz radiation" Rep. Prog. Phys., vol.70, pp.1325-1379, 2007. [2] I. Catapano, F. Soldovieri, "THz imaging and spectroscopy: First experiments and preliminary results", Proceeding of 8th Int. Workshop on Advanced Ground Penetrating Radar (IWAGPR 2015), 4pp., 2015.

  16. Confocal Imaging of Biological Tissues Using Second Harmonic Generation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, B-M.; Stoller, P.; Reiser, K.; Eichler, J.; Yan, M.; Rubenchik, A.; Da Silva, L.

    2000-03-06

    A confocal microscopy imaging system was devised to selectively detect Second harmonic signals generated by biological tissues. Several types of biological tissues were examined using this imaging system, including human teeth, bovine blood vessels, and chicken skin. All these tissues generated strong second harmonic signals. There is considerable evidence that the source of these signals in tissue is collagen. Collagen, the predominant component of most tissues, is known to have second order nonlinear susceptibility. This technique may have diagnostic usefulness in pathophysiological conditions characterized by changes in collagen structure including malignant transformation of nevi, progression of diabetic complications, and abnormalities in wound healing.

  17. Classification of biological and non-biological fluvial particles using image processing and artificial neural network

    Science.gov (United States)

    Shrestha, Bim Prasad; Shrestha, Nabin Kumar; Poudel, Laxman

    2009-04-01

    Particles flowing along with water largely affect safe drinking water, irrigation, aquatic life preservation and hydropower generation. This research describes activities that lead to development of fluvial particle characterization that includes detection of biological and non-biological particles and shape characterization using Image Processing and Artificial Neural Network (ANN). Fluvial particles are characterized based on multi spectral images processing using ANN. Images of wavelength of 630nm and 670nm are taken as most distinctive characterizing properties of biological and non-biological particles found in Bagmati River of Nepal. The samples were collected at pre-monsoon, monsoon and post-monsoon seasons. Random samples were selected and multi spectral images are processed using MATLAB 6.5. Thirty matrices were built from each sample. The obtained data of 42 rows and 60columns were taken as input training with an output matrix of 42 rows and 2 columns. Neural Network of Perceptron model was created using a transfer function. The system was first validated and later on tested at 18 different strategic locations of Bagmati River of Kathmandu Valley, Nepal. This network classified biological and non biological particles. Development of new non-destructive technique to characterize biological and non-biological particles from fluvial sample in a real time has a significance breakthrough. This applied research method and outcome is an attractive model for real time monitoring of particles and has many applications that can throw a significant outlet to many researches and for effective utilization of water resources. It opened a new horizon of opportunities for basic and applied research at Kathmandu University in Nepal.

  18. Statistical analysis of joint toxicity in biological growth experiments

    DEFF Research Database (Denmark)

    Spliid, Henrik; Tørslev, J.

    1994-01-01

    The authors formulate a model for the analysis of designed biological growth experiments where a mixture of toxicants is applied to biological target organisms. The purpose of such experiments is to assess the toxicity of the mixture in comparison with the toxicity observed when the toxicants...... are applied individually to the organisms. The analysis is based on a random differential equation describing the growth of the organisms. This model yields a natural measure of interaction between toxicants and the hypothesis of independent action from a mixture of toxicants can be tested. The proposed model...

  19. Method and apparatus to image biological interactions in plants

    Science.gov (United States)

    Weisenberger, Andrew; Bonito, Gregory M.; Reid, Chantal D.; Smith, Mark Frederick

    2015-12-22

    A method to dynamically image the actual translocation of molecular compounds of interest in a plant root, root system, and rhizosphere without disturbing the root or the soil. The technique makes use of radioactive isotopes as tracers to label molecules of interest and to image their distribution in the plant and/or soil. The method allows for the study and imaging of various biological and biochemical interactions in the rhizosphere of a plant, including, but not limited to, mycorrhizal associations in such regions.

  20. Visualization of biological texture using correlation coefficient images.

    Science.gov (United States)

    Sviridov, Alexander P; Ulissi, Zachary; Chernomordik, Victor; Hassan, Moinuddin; Gandjbakhche, Amir H

    2006-01-01

    Subsurface structural features of biological tissue are visualized using polarized light images. The technique of Pearson correlation coefficient analysis is used to reduce blurring of these features by unpolarized backscattered light and to visualize the regions of high statistical similarities within the noisy tissue images. It is shown that under certain conditions, such correlation coefficient maps are determined by the textural character of tissues and not by the chosen region of interest, providing information on tissue structure. As an example, the subsurface texture of a demineralized tooth sample is enhanced from a noisy polarized light image.

  1. Molecular probes for nonlinear optical imaging of biological membranes

    Science.gov (United States)

    Blanchard-Desce, Mireille H.; Ventelon, Lionel; Charier, Sandrine; Moreaux, Laurent; Mertz, Jerome

    2001-12-01

    Second-harmonic generation (SHG) and two-photon excited fluorescence (TPEF) are nonlinear optical (NLO) phenomena that scale with excitation intensity squared, and hence give rise to an intrinsic 3-dimensional resolution when used in microscopic imaging. TPEF microscopy has gained widespread popularity in the biology community whereas SHG microscopy promises to be a powerful tool because of its sensitivity to local asymmetry. We have implemented an approach toward the design of NLO-probes specifically adapted for SHG and/or TPEF imaging of biological membranes. Our strategy is based on the design of nanoscale amphiphilic NLO-phores. We have prepared symmetrical bolaamphiphilic fluorophores combining very high two-photon absorption (TPA) cross-sections in the visible red region and affinity for cellular membranes. Their incorporation and orientation in lipid membranes can be monitored via TPEF anisotropy. We have also prepared amphiphilic push-pull chromophores exhibiting both large TPA cross-sections and very large first hyperpolarizabilities in the near-IR region. These NLO-probes have proved to be particularly useful for imaging of biological membranes by simultaneous SHG and TPEF microscopy and offer attractive prospects for real-time imaging of fundamental biological processes such as adhesion, fusion or reporting of membrane potentials.

  2. Fluorescent Dendrimer Nanoconjugates as Advanced Probes for Biological Imaging

    Science.gov (United States)

    Reilly, Daniel; Kim, Sung Hoon; Katzenellenbogen, John A.; Schroeder, Charles M.

    2014-03-01

    Recent advances in fluorescence microscopy have enabled improvements in spatial resolution for biological imaging. However, there is a strong need for development of advanced fluorescent probes to enable a molecular-scale understanding of biological events. In this work, we report the development of a new class of probes for fluorescence imaging based on dye-conjugated dendrimer nanoconjugates. We utilize molecular-scale dendritic scaffolds as fluorescent probes, thereby enabling conjugation of multiple dyes and linkers to the scaffold periphery. In particular, we use polyamidoamine dendrimers as molecular scaffolds, wherein dye conjugation can be varied over a wide range. Single molecule fluorescence imaging shows that dendrimer nanoconjugates are far brighter than single fluorophores, resulting in increased localization precision. In addition, we further developed a new set of remarkably photostable probes by conjugating photoprotective triplet state quenchers directly onto the dendritic scaffold. We observe large increases in the photobleaching times compared to single dyes and reduced transient dark states (blinking). Overall, we believe that these new probes will allow for single molecule imaging over long time scales, enabling new vistas in biological imaging.

  3. Standard reporting requirements for biological samples in metabolomics experiments: Microbial and in vitro biology experiments

    NARCIS (Netherlands)

    Werf, M.J. van der; Takors, R.; Smedsgaard, J.; Nielsen, J.; Ferenci, T.; Portais, J.C.; Wittmann, C.; Hooks, M.; Tomassini, A.; Oldiges, M.; Fostel, J.; Sauer, U.

    2007-01-01

    With the increasing use of metabolomics as a means to study a large number of different biological research questions, there is a need for a minimal set of reporting standards that allow the scientific community to evaluate, understand, repeat, compare and re-investigate metabolomics studies. Here w

  4. Volume scanning electron microscopy for imaging biological ultrastructure.

    Science.gov (United States)

    Titze, Benjamin; Genoud, Christel

    2016-11-01

    Electron microscopy (EM) has been a key imaging method to investigate biological ultrastructure for over six decades. In recent years, novel volume EM techniques have significantly advanced nanometre-scale imaging of cells and tissues in three dimensions. Previously, this had depended on the slow and error-prone manual tasks of cutting and handling large numbers of sections, and imaging them one-by-one with transmission EM. Now, automated volume imaging methods mostly based on scanning EM (SEM) allow faster and more reliable acquisition of serial images through tissue volumes and achieve higher z-resolution. Various software tools have been developed to manipulate the acquired image stacks and facilitate quantitative analysis. Here, we introduce three volume SEM methods: serial block-face electron microscopy (SBEM), focused ion beam SEM (FIB-SEM) and automated tape-collecting ultramicrotome SEM (ATUM-SEM). We discuss and compare their capabilities, provide an overview of the full volume SEM workflow for obtaining 3D datasets and showcase different applications for biological research.

  5. Implied Movement in Static Images Reveals Biological Timing Processing

    Directory of Open Access Journals (Sweden)

    Francisco Carlos Nather

    2015-08-01

    Full Text Available Visual perception is adapted toward a better understanding of our own movements than those of non-conspecifics. The present study determined whether time perception is affected by pictures of different species by considering the evolutionary scale. Static (“S” and implied movement (“M” images of a dog, cheetah, chimpanzee, and man were presented to undergraduate students. S and M images of the same species were presented in random order or one after the other (S-M or M-S for two groups of participants. Movement, Velocity, and Arousal semantic scales were used to characterize some properties of the images. Implied movement affected time perception, in which M images were overestimated. The results are discussed in terms of visual motion perception related to biological timing processing that could be established early in terms of the adaptation of humankind to the environment.

  6. The Galileo Solid-State Imaging experiment

    Science.gov (United States)

    Belton, M.J.S.; Klaasen, K.P.; Clary, M.C.; Anderson, J.L.; Anger, C.D.; Carr, M.H.; Chapman, C.R.; Davies, M.E.; Greeley, R.; Anderson, D.; Bolef, L.K.; Townsend, T.E.; Greenberg, R.; Head, J. W.; Neukum, G.; Pilcher, C.B.; Veverka, J.; Gierasch, P.J.; Fanale, F.P.; Ingersoll, A.P.; Masursky, H.; Morrison, D.; Pollack, James B.

    1992-01-01

    The Solid State Imaging (SSI) experiment on the Galileo Orbiter spacecraft utilizes a high-resolution (1500 mm focal length) television camera with an 800 ?? 800 pixel virtual-phase, charge-coupled detector. It is designed to return images of Jupiter and its satellites that are characterized by a combination of sensitivity levels, spatial resolution, geometric fiedelity, and spectral range unmatched by imaging data obtained previously. The spectral range extends from approximately 375 to 1100 nm and only in the near ultra-violet region (??? 350 nm) is the spectral coverage reduced from previous missions. The camera is approximately 100 times more sensitive than those used in the Voyager mission, and, because of the nature of the satellite encounters, will produce images with approximately 100 times the ground resolution (i.e., ??? 50 m lp-1) on the Galilean satellites. We describe aspects of the detector including its sensitivity to energetic particle radiation and how the requirements for a large full-well capacity and long-term stability in operating voltages led to the choice of the virtual phase chip. The F/8.5 camera system can reach point sources of V(mag) ??? 11 with S/N ??? 10 and extended sources with surface brightness as low as 20 kR in its highest gain state and longest exposure mode. We describe the performance of the system as determined by ground calibration and the improvements that have been made to the telescope (same basic catadioptric design that was used in Mariner 10 and the Voyager high-resolution cameras) to reduce the scattered light reaching the detector. The images are linearly digitized 8-bits deep and, after flat-fielding, are cosmetically clean. Information 'preserving' and 'non-preserving' on-board data compression capabilities are outlined. A special "summation" mode, designed for use deep in the Jovian radiation belts, near Io, is also described. The detector is 'preflashed' before each exposure to ensure the photometric linearity

  7. Maximizing the information content of experiments in systems biology.

    Directory of Open Access Journals (Sweden)

    Juliane Liepe

    Full Text Available Our understanding of most biological systems is in its infancy. Learning their structure and intricacies is fraught with challenges, and often side-stepped in favour of studying the function of different gene products in isolation from their physiological context. Constructing and inferring global mathematical models from experimental data is, however, central to systems biology. Different experimental setups provide different insights into such systems. Here we show how we can combine concepts from Bayesian inference and information theory in order to identify experiments that maximize the information content of the resulting data. This approach allows us to incorporate preliminary information; it is global and not constrained to some local neighbourhood in parameter space and it readily yields information on parameter robustness and confidence. Here we develop the theoretical framework and apply it to a range of exemplary problems that highlight how we can improve experimental investigations into the structure and dynamics of biological systems and their behavior.

  8. Maximizing the information content of experiments in systems biology.

    Science.gov (United States)

    Liepe, Juliane; Filippi, Sarah; Komorowski, Michał; Stumpf, Michael P H

    2013-01-01

    Our understanding of most biological systems is in its infancy. Learning their structure and intricacies is fraught with challenges, and often side-stepped in favour of studying the function of different gene products in isolation from their physiological context. Constructing and inferring global mathematical models from experimental data is, however, central to systems biology. Different experimental setups provide different insights into such systems. Here we show how we can combine concepts from Bayesian inference and information theory in order to identify experiments that maximize the information content of the resulting data. This approach allows us to incorporate preliminary information; it is global and not constrained to some local neighbourhood in parameter space and it readily yields information on parameter robustness and confidence. Here we develop the theoretical framework and apply it to a range of exemplary problems that highlight how we can improve experimental investigations into the structure and dynamics of biological systems and their behavior.

  9. Macro-/micro-environment-sensitive chemosensing and biological imaging.

    Science.gov (United States)

    Yang, Zhigang; Cao, Jianfang; He, Yanxia; Yang, Jung Ho; Kim, Taeyoung; Peng, Xiaojun; Kim, Jong Seung

    2014-07-01

    Environment-related parameters, including viscosity, polarity, temperature, hypoxia, and pH, play pivotal roles in controlling the physical or chemical behaviors of local molecules. In particular, in a biological environment, such factors predominantly determine the biological properties of the local environment or reflect corresponding status alterations. Abnormal changes in these factors would cause cellular malfunction or become a hallmark of the occurrence of severe diseases. Therefore, in recent years, they have increasingly attracted research interest from the fields of chemistry and biological chemistry. With the emergence of fluorescence sensing and imaging technology, several fluorescent chemosensors have been designed to respond to such parameters and to further map their distributions and variations in vitro/in vivo. In this work, we have reviewed a number of various environment-responsive chemosensors related to fluorescent recognition of viscosity, polarity, temperature, hypoxia, and pH that have been reported thus far.

  10. Nonlinear plasmonic imaging techniques and their biological applications

    Science.gov (United States)

    Deka, Gitanjal; Sun, Chi-Kuang; Fujita, Katsumasa; Chu, Shi-Wei

    2017-01-01

    Nonlinear optics, when combined with microscopy, is known to provide advantages including novel contrast, deep tissue observation, and minimal invasiveness. In addition, special nonlinearities, such as switch on/off and saturation, can enhance the spatial resolution below the diffraction limit, revolutionizing the field of optical microscopy. These nonlinear imaging techniques are extremely useful for biological studies on various scales from molecules to cells to tissues. Nevertheless, in most cases, nonlinear optical interaction requires strong illumination, typically at least gigawatts per square centimeter intensity. Such strong illumination can cause significant phototoxicity or even photodamage to fragile biological samples. Therefore, it is highly desirable to find mechanisms that allow the reduction of illumination intensity. Surface plasmon, which is the collective oscillation of electrons in metal under light excitation, is capable of significantly enhancing the local field around the metal nanostructures and thus boosting up the efficiency of nonlinear optical interactions of the surrounding materials or of the metal itself. In this mini-review, we discuss the recent progress of plasmonics in nonlinear optical microscopy with a special focus on biological applications. The advancement of nonlinear imaging modalities (including incoherent/coherent Raman scattering, two/three-photon luminescence, and second/third harmonic generations that have been amalgamated with plasmonics), as well as the novel subdiffraction limit imaging techniques based on nonlinear behaviors of plasmonic scattering, is addressed.

  11. Nonlinear plasmonic imaging techniques and their biological applications

    Directory of Open Access Journals (Sweden)

    Deka Gitanjal

    2016-07-01

    Full Text Available Nonlinear optics, when combined with microscopy, is known to provide advantages including novel contrast, deep tissue observation, and minimal invasiveness. In addition, special nonlinearities, such as switch on/off and saturation, can enhance the spatial resolution below the diffraction limit, revolutionizing the field of optical microscopy. These nonlinear imaging techniques are extremely useful for biological studies on various scales from molecules to cells to tissues. Nevertheless, in most cases, nonlinear optical interaction requires strong illumination, typically at least gigawatts per square centimeter intensity. Such strong illumination can cause significant phototoxicity or even photodamage to fragile biological samples. Therefore, it is highly desirable to find mechanisms that allow the reduction of illumination intensity. Surface plasmon, which is the collective oscillation of electrons in metal under light excitation, is capable of significantly enhancing the local field around the metal nanostructures and thus boosting up the efficiency of nonlinear optical interactions of the surrounding materials or of the metal itself. In this mini-review, we discuss the recent progress of plasmonics in nonlinear optical microscopy with a special focus on biological applications. The advancement of nonlinear imaging modalities (including incoherent/coherent Raman scattering, two/three-photon luminescence, and second/third harmonic generations that have been amalgamated with plasmonics, as well as the novel subdiffraction limit imaging techniques based on nonlinear behaviors of plasmonic scattering, is addressed.

  12. Biological object recognition in μ-radiography images

    Science.gov (United States)

    Prochazka, A.; Dammer, J.; Weyda, F.; Sopko, V.; Benes, J.; Zeman, J.; Jandejsek, I.

    2015-03-01

    This study presents an applicability of real-time microradiography to biological objects, namely to horse chestnut leafminer, Cameraria ohridella (Insecta: Lepidoptera, Gracillariidae) and following image processing focusing on image segmentation and object recognition. The microradiography of insects (such as horse chestnut leafminer) provides a non-invasive imaging that leaves the organisms alive. The imaging requires a high spatial resolution (micrometer scale) radiographic system. Our radiographic system consists of a micro-focus X-ray tube and two types of detectors. The first is a charge integrating detector (Hamamatsu flat panel), the second is a pixel semiconductor detector (Medipix2 detector). The latter allows detection of single quantum photon of ionizing radiation. We obtained numerous horse chestnuts leafminer pupae in several microradiography images easy recognizable in automatic mode using the image processing methods. We implemented an algorithm that is able to count a number of dead and alive pupae in images. The algorithm was based on two methods: 1) noise reduction using mathematical morphology filters, 2) Canny edge detection. The accuracy of the algorithm is higher for the Medipix2 (average recall for detection of alive pupae =0.99, average recall for detection of dead pupae =0.83), than for the flat panel (average recall for detection of alive pupae =0.99, average recall for detection of dead pupae =0.77). Therefore, we conclude that Medipix2 has lower noise and better displays contours (edges) of biological objects. Our method allows automatic selection and calculation of dead and alive chestnut leafminer pupae. It leads to faster monitoring of the population of one of the world's important insect pest.

  13. Hydralab+: Representing timescales of biological change in flume experiments

    Science.gov (United States)

    Baynes, Edwin; McLelland, Stuart; Parsons, Daniel

    2016-04-01

    Fluvial environments are vulnerable to future climate change due to non-linear responses to shifts in boundary conditions such as a migration to a hydrological regime characterised by more frequent extreme events. The biological component of these systems is critical for understanding the morphodynamic responses since organisms are often at the interface between water and sediment transport systems. Under a changing climate, the growth or decline of a particular species may change the flow dynamics and/or sediment transport. Hence, flume experiments that seek to accurately model the impact of climate change on the morphodynamics of sedimentary systems should consider the interaction between organisms and climate-induced changes in hydrodynamic forcing. This requires the ability to control and/or mimic biological components within flume experiments on timescales that are compatible with climate change forcing. Here, we present a review of existing research covering morphodynamics-biological interactions in flume experiments. We consider the approaches implemented to scale organisms (e.g. small-scale or chemical surrogates) and how these can be used to represent variations in the biological component over different timescales. Disparities in the scaling of hydrodynamics, morphodynamics and biota using these existing approaches are identified. During Hydralab+, this review will form the basis to develop innovative experimental protocols to represent total system response to climate change within a laboratory setting (e.g. developing new surrogates that can capture biological responses to climate forcing and enable modelling of longer time periods and longer-term trends). This will allow an improved understanding of the impact of climate change to be developed and potentially guide future adaptation strategies.

  14. The use of contrast agent for imaging biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Dammer, J; Sopko, V; Jakubek, J [Institute of Experimental and Applied Physics, Czech Technical University in Prague, Horska 3a/22, CZ 12800 Prague 2 (Czech Republic); Weyda, F, E-mail: jiri.dammer@utef.cvut.cz [Biological center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Branisovska 31, CZ-37005 Ceske Budejovice (Czech Republic)

    2011-01-15

    The technique of X-ray transmission imaging has been available for over a century and is still among the fastest and easiest approaches to the studies of internal structure of biological samples. Recent advances in semiconductor technology have led to the development of new types of X-ray detectors with direct conversion of interacting X-ray photon to an electric signal. Semiconductor pixel detectors seem to be specially promising; compared to the film technique, they provide single-quantum and real-time digital information about the objects being studied. We describe the recently developed radiographic apparatus, equipped with Medipix2 semiconductor pixel detector. The detector is used as an imager that counts individual photons of ionizing radiation, emitted by an X-ray tube (micro- or nano-focus FeinFocus). Thanks to the wide dynamic range of the Medipix2 detector and its high spatial resolution better than 1{mu}m, the setup is particularly suitable for radiographic imaging of small biological samples, including in-vivo observations with contrast agent (Optiray). Along with the description of the apparatus we provide examples of the use iodine contrast agent as a tracer in various insects as model organisms. The motivation of our work is to develop our imaging techniques as non-destructive and non-invasive. Microradiographic imaging helps detect organisms living in a not visible environment, visualize the internal biological processes and also to resolve the details of their body (morphology). Tiny live insects are an ideal object for our studies.

  15. A national comparison of biochemistry and molecular biology capstone experiences.

    Science.gov (United States)

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices.

  16. Laser desorption postionization for imaging MS of biological material.

    Science.gov (United States)

    Akhmetov, Artem; Moore, Jerry F; Gasper, Gerald L; Koin, Peter J; Hanley, Luke

    2010-02-01

    Vacuum ultraviolet single photon ionization (VUV SPI) is a soft ionization technique that has the potential to address many of the limitations of matrix-assisted laser desorption/ionization (MALDI) for imaging MS. Laser desorption postionization (LDPI) uses VUV SPI for postionization and is experimentally analogous to a MALDI instrument with the addition of a pulsed VUV light source. This review discusses progress in LDPI-MS over the last decade, with an emphasis on imaging MS of bacterial biofilms, analytes whose high salt environment make them particularly resistant to imaging by MALDI-MS. This review first considers fundamental aspects of VUV SPI including ionization mechanisms, cross sections, quantum yields of ionization, dissociation and potential mass limits. The most common sources of pulsed VUV radiation are then described along with a newly constructed LDPI-MS instrument with imaging capabilities. Next, the detection and imaging of small molecules within intact biofilms is demonstrated by LDPI-MS using 7.87 eV (157.6 nm) VUV photons from a molecular fluorine excimer laser, followed by the use of aromatic tags for detection of selected species within the biofilm. The final section considers the future prospects for imaging intact biological samples by LDPI-MS. Copyright 2010 John Wiley & Sons, Ltd.

  17. THz near-field imaging of biological tissues employing synchrotronradiation

    Energy Technology Data Exchange (ETDEWEB)

    Schade, Ulrich; Holldack, Karsten; Martin, Michael C.; Fried,Daniel

    2004-12-23

    Terahertz scanning near-field infrared microscopy (SNIM) below 1 THz is demonstrated. The near-field technique benefits from the broadband and highly brilliant coherent synchrotron radiation (CSR) from an electron storage ring and from a detection method based on locking onto the intrinsic time structure of the synchrotron radiation. The scanning microscope utilizes conical wave guides as near-field probes with apertures smaller than the wavelength. Different cone approaches have been investigated to obtain maximum transmittance. Together with a Martin-Puplett spectrometer the set-up enables spectroscopic mapping of the transmittance of samples well below the diffraction limit. Spatial resolution down to about lambda/40 at 2 wavenumbers (0.06 THz) is derived from the transmittance spectra of the near-field probes. The potential of the technique is exemplified by imaging biological samples. Strongly absorbing living leaves have been imaged in transmittance with a spatial resolution of 130 mu-m at about 12 wave numbers (0.36 THz). The THz near-field images reveal distinct structural differences of leaves from different plants investigated. The technique presented also allows spectral imaging of bulky organic tissues. Human teeth samples of various thicknesses have been imaged between 2 and 20 wavenumbers (between 0.06and 0.6 THz). Regions of enamel and dentin within tooth samples are spatially and spectrally resolved, and buried caries lesions are imaged through both the outer enamel and into the underlying dentin.

  18. Why the long face? The importance of vertical image structure for biological "barcodes" underlying face recognition.

    Science.gov (United States)

    Spence, Morgan L; Storrs, Katherine R; Arnold, Derek H

    2014-07-29

    Humans are experts at face recognition. The mechanisms underlying this complex capacity are not fully understood. Recently, it has been proposed that face recognition is supported by a coarse-scale analysis of visual information contained in horizontal bands of contrast distributed along the vertical image axis-a biological facial "barcode" (Dakin & Watt, 2009). A critical prediction of the facial barcode hypothesis is that the distribution of image contrast along the vertical axis will be more important for face recognition than image distributions along the horizontal axis. Using a novel paradigm involving dynamic image distortions, a series of experiments are presented examining famous face recognition impairments from selectively disrupting image distributions along the vertical or horizontal image axes. Results show that disrupting the image distribution along the vertical image axis is more disruptive for recognition than matched distortions along the horizontal axis. Consistent with the facial barcode hypothesis, these results suggest that human face recognition relies disproportionately on appropriately scaled distributions of image contrast along the vertical image axis.

  19. CUTIE: Cubesat Ultraviolet Transient Imaging Experiment

    Science.gov (United States)

    Cenko, Stephen B.; Bellm, Eric Christopher; Gal-Yam, Avishay; Gezari, Suvi; Gorjian, Varoujan; Jewell, April; Kruk, Jeffrey W.; Kulkarni, Shrinivas R.; Mushotzky, Richard; Nikzad, Shouleh; Piro, Anthony; Waxman, Eli; Ofek, Eran Oded

    2017-01-01

    We describe a mission concept for the Cubesat Ultraviolet Transient Imaging Experiment (CUTIE). CUTIE will image an area on the sky of ~ 1700 square degrees every ~ 95 min at near-UV wavelengths (260-320 nm) to a depth of 19.0 mag (AB). These capabilities represent orders of magnitude improvement over past UV imagers, allowing CUTIE to conduct the first true synoptic survey of the transient and variable sky in the UV bandpass. CUTIE will uniquely address key Decadal Survey science questions such as how massive stars end their lives, how super-massive black holes accrete material and influence their surroundings, and how suitable habitable-zone planets around low-mass stars are for hosting life. By partnering with upcoming ground-based time-domain surveys, CUTIE will further leverage its low-Earth orbit to provide a multi-wavelength view of the dynamic universe that can only be achieved from space. The remarkable sensitivity for such a small payload is achieved via the use of large format delta-doped CCDs; space qualifying this technology will serve as a key milestone towards the development of future large missions (Explorers and Surveyors). Finally, our innovative design in a 6U cubesat form factor will enable significant cost savings, accelerating the timeline from conception to on-sky operation (5 years; well matched for graduate student participation).

  20. Biological effects of exposure to magnetic resonance imaging: an overview

    Directory of Open Access Journals (Sweden)

    Formica Domenico

    2004-04-01

    Full Text Available Abstract The literature on biological effects of magnetic and electromagnetic fields commonly utilized in magnetic resonance imaging systems is surveyed here. After an introduction on the basic principles of magnetic resonance imaging and the electric and magnetic properties of biological tissues, the basic phenomena to understand the bio-effects are described in classical terms. Values of field strengths and frequencies commonly utilized in these diagnostic systems are reported in order to allow the integration of the specific literature on the bio-effects produced by magnetic resonance systems with the vast literature concerning the bio-effects produced by electromagnetic fields. This work gives an overview of the findings about the safety concerns of exposure to static magnetic fields, radio-frequency fields, and time varying magnetic field gradients, focusing primarily on the physics of the interactions between these electromagnetic fields and biological matter. The scientific literature is summarized, integrated, and critically analyzed with the help of authoritative reviews by recognized experts, international safety guidelines are also cited.

  1. The Climate Experiences of Students in Introductory Biology

    Directory of Open Access Journals (Sweden)

    Ramón S. Barthelemy

    2015-08-01

    Full Text Available Understanding course climate is important for improving students’ experiences and increasing the likelihood of their persistence in STEM fields. This study presents climate survey results from 523 students taking introductory biology at the University of Michigan. Principal component analysis revealed that a student’s climate experience is comprised of five main elements: comfort, school avoidance, relationship to course, academic stress, and discomfort. Of these climate factors, comfort, school avoidance, and relationship to course were significant predictors of course satisfaction, and academic stress was a significant predictor of persistence. The results indicated the importance of a positive climate that is facilitated by the instructor in order to promote a positive student experience. Climate may be an important metric for institutions to track across time and course.

  2. CT imaging of enhanced oil recovery experiments

    Energy Technology Data Exchange (ETDEWEB)

    Gall, B.L.

    1992-12-01

    X-ray computerized tomography (Cr) has been used to study fluid distributions during chemical enhanced oil recovery experiments. Four CT-monitored corefloods were conducted, and oil saturation distributions were calculated at various stages of the experiments. Results suggested that this technique could add significant information toward interpretation and evaluation of surfactant/polymer EOR recovery methods. CT-monitored tracer tests provided information about flow properties in the core samples. Nonuniform fluid advance could be observed, even in core that appeared uniform by visual inspection. Porosity distribution maps based on CT density calculations also showed the presence of different porosity layers that affected fluid movement through the cores. Several types of CT-monitored corefloods were conducted. Comparisons were made for CT-monitored corefloods using chemical systems that were highly successful in reducing residual oil saturations in laboratory experiments and less successful systems. Changes were made in surfactant formulation and in concentration of the mobility control polymer. Use of a poor mobility control agent failed to move oil that was not initially displaced by the injected surfactant solution; even when a good'' surfactant system was used. Use of a less favorable surfactant system with adequate mobility control could produce as much oil as the use of a good surfactant system with inadequate mobility control. The role of mobility control, therefore, becomes a critical parameter for successful application of chemical EOR. Continuation of efforts to use CT imaging in connection with chemical EOR evaluations is recommended.

  3. CT imaging of enhanced oil recovery experiments

    Energy Technology Data Exchange (ETDEWEB)

    Gall, B.L.

    1992-12-01

    X-ray computerized tomography (Cr) has been used to study fluid distributions during chemical enhanced oil recovery experiments. Four CT-monitored corefloods were conducted, and oil saturation distributions were calculated at various stages of the experiments. Results suggested that this technique could add significant information toward interpretation and evaluation of surfactant/polymer EOR recovery methods. CT-monitored tracer tests provided information about flow properties in the core samples. Nonuniform fluid advance could be observed, even in core that appeared uniform by visual inspection. Porosity distribution maps based on CT density calculations also showed the presence of different porosity layers that affected fluid movement through the cores. Several types of CT-monitored corefloods were conducted. Comparisons were made for CT-monitored corefloods using chemical systems that were highly successful in reducing residual oil saturations in laboratory experiments and less successful systems. Changes were made in surfactant formulation and in concentration of the mobility control polymer. Use of a poor mobility control agent failed to move oil that was not initially displaced by the injected surfactant solution; even when a ``good`` surfactant system was used. Use of a less favorable surfactant system with adequate mobility control could produce as much oil as the use of a good surfactant system with inadequate mobility control. The role of mobility control, therefore, becomes a critical parameter for successful application of chemical EOR. Continuation of efforts to use CT imaging in connection with chemical EOR evaluations is recommended.

  4. Prospective of ultradispersic magnetic particles in biological experiments in microgravity

    Science.gov (United States)

    Nechitailo, Galina S.; Kuznetsov, Anatoli; Malashin, S.

    All organisms on Earth use gravity for their lifecycles. Microgravity disturbs the lifecycles significantly: orientation ability is damaged, thermo and mass exchange processes are changed, adaptation mechanisms are destroyed. A recovering the normal life cycle of organism in future long-term mission requires an artificial gravity which is complicate and not realistic with present technologies. We propose to use a magnetic properties of the biological objects for recovering of the gravity-dependent biological processes in organism during space flight. Based on result of magnetic properties investigation in gravity-sensitive plant cells, we have prepared and carried out the experiments on space station MIR. For the experiments, Magnitogravistat device was designed and installed on the station. The aim of the experiment was to replace a gravity factor of plant with a magnetic factor. The magnetic effect is based on the fact, that a magnetic particle of V volume is under the force F=ΔæVHgradH in the magnetic gradient gradH, where Δæ is the difference between the magnetic susceptibility of particle and media. When the particles are placed into the cell, the cell can be managed by the magnetic field. In laboratory experiment the iron-carbon particles of 1-2 um with nanostructurised surface and high adsorption properties have been used. The particles can be suspended in water and adsorbed chemicals including cell metabolites. In strong magnetic field, the particles can be agglomerated and the liquid substrate can be replaced. The local magnetic field near the particles can influence on cell processes. The magnetic field causes a cell differentiation and can influence on cell proliferation. A new space experiment with magnetic particles is planned to get a knowledge on cell influence and to improve a cell metabolism.

  5. It is an Experience, Not a Lesson: The Nature of High School Students' Experiences at a Biological Field Station

    Science.gov (United States)

    Behrendt, Marc E.

    The purpose of this case study was to describe the nature of high school students' experiences in the immersive four-day field experience at Stone Laboratory Biological Field Station including excursions to Kelley's Island and South Bass Island. Six tenth, eleventh, and twelfth grade students participated through interviews, photovoice, observations, and a survey. Pretrip semi-structured interviews were conducted to understand each participant student's relationship with science. Participants were given cameras to record their field trip experiences to relate what they found interesting, important, and exciting. Back at school after the field trip, the participants were asked to choose their five most meaningful photographs, and write a short essay to describe the significance of each image. A posttrip semi-structured interview explored each participant's experiences during the field trip. An unstructured interview was conducted to discuss each participant's full photograph gallery from the field trip. Interview transcripts were member checked with one minor wording change. Analysis consisted of open coding using apriori codes derived from the ecological framework and emergent codes derived from the data. Coding was duplicated through multiple readers. Significant findings included: 1) Prior experience, prior knowledge, and funds of knowledge added relevance and value to an experience, facilitating interest development; 2) Experiences appeared to be more meaningful when all the senses were stimulated; 3) Friends and peers were an essential part of a quality experience; 4) Quality experiences included a wow factor, or sudden awareness; 5) Teachers needed to be within the experience, not the focus of the experience, and needed to be available to answer questions, be enthusiastic when a discovery was made, and promote student reflection concerning their perceptions and discoveries; 6) A quality informal learning situation incorporated the cognitive/affective, physical

  6. [Equipment for biological experiments with snails aboard piloted orbital stations].

    Science.gov (United States)

    Gorgiladze, G I; Korotkova, E V; Kuznetsova, E E; Mukhamedieva, L N; Begrov, V V; Pepeliaev, Iu V

    2010-01-01

    To fly biological experiments aboard piloted orbital stations, research equipment was built up of an incubation container, filter system and automatic temperature controller. Investigations included analysis of the makeup and concentrations of gases produced by animals (snails) during biocycle, and emitted after death. Filters are chemisorption active fibrous materials (AFM) with high sorption rate and water receptivity (cation exchange fiber VION-KN-1 and anion exchange fiber VION-AS-1), and water-repellent carbon adsorbent SKLTS. AFM filters were effective in air cleaning and practically excluded ingress of chemical substances from the container into cabin atmosphere over more than 100 days.

  7. Combining Different Modalities for 3D Imaging of Biological Objects

    CERN Document Server

    Tsyganov, E; Kulkarni, P; Mason, R; Parkey, R; Seliuonine, S; Shay, J; Soesbe, T; Zhezher, V; Zinchenko, A I

    2005-01-01

    A resolution enhanced NaI(Tl)-scintillator micro-SPECT device using pinhole collimator geometry has been built and tested with small animals. This device was constructed based on a depth-of-interaction measurement using a thick scintillator crystal and a position sensitive PMT to measure depth-dependent scintillator light profiles. Such a measurement eliminates the parallax error that degrades the high spatial resolution required for small animal imaging. This novel technique for 3D gamma-ray detection was incorporated into the micro-SPECT device and tested with a $^{57}$Co source and $^{98m}$Tc-MDP injected in mice body. To further enhance the investigating power of the tomographic imaging different imaging modalities can be combined. In particular, as proposed and shown in this paper, the optical imaging permits a 3D reconstruction of the animal's skin surface thus improving visualization and making possible depth-dependent corrections, necessary for bioluminescence 3D reconstruction in biological objects. ...

  8. BIOMEX (Biology and Mars Experiment): Preliminary results on Antarctic black cryptoendolithic fungi in ground based experiments

    OpenAIRE

    C. Pacelli; Selbmann, L.; S. Onofri; de Vera, J.P.P.

    2014-01-01

    The main goal for astrobiologists is to find traces of present or past life in extraterrestrial environment or in meteorites. Biomolecules, such as lipids, pigments or polysaccharides, may be useful to establish the presence of extant or extinct life (Simoneit, B et al., 1998). BIOMEX (Biology and Mars Experiment) aims to measure to what extent biomolecules, such as pigments and cellular components, preserve their stability under space and Mars-like conditions. The experiment has just been la...

  9. Biological wound dressings sterilized with gamma radiation: Mexican clinical experience

    Science.gov (United States)

    Martínez-Pardo, M. E.; Ley-Chávez, E.; Reyes-Frías, M. L.; Rodríguez-Ferreyra, P.; Vázquez-Maya, L.; Salazar, M. A.

    2007-11-01

    Biological wound dressings sterilized with gamma radiation, such as amnion and pig skin, are a reality in Mexico. These tissues are currently processed in the tissue bank and sterilized in the Gamma Industrial Irradiation Plant; both facilities belong to the Instituto Nacional de Investigaciones Nucleares (ININ) (National Institute of Nuclear Research). With the strong support of the International Atomic Energy Agency, the bank was established at the ININ and the Mexican Ministry of Health issued its sanitary license on July 7, 1999. The Quality Management System of the bank was certified by ISO 9001:2000 on August 1, 2003; the scope of the system is "Research, Development and Processing of Biological Tissues Sterilized with Gamma Radiation". At present, more than 150 patients from 16 hospitals have been successfully treated with these tissues. This paper presents a brief description of the tissue processing, as well as the present Mexican clinical experience with children and adult patients who underwent medical treatment with radiosterilized amnion and pig skin, used as biological wound dressings on burns and ocular surface disorders.

  10. Elucidating GPR Response to Biological Activity: Field and Laboratory Experiments

    Science.gov (United States)

    Tsoflias, G. P.; Schillig, P. C.; McGlashan, M. A.; Roberts, J. A.; Devlin, J. F.

    2010-12-01

    Recent studies of the geophysical signatures of biological processes in earth environments have resulted in the emergent field of “biogeophysics”. The ability to monitor remotely and to quantify active biological processes in the subsurface can have transformative implications to a wide range of investigations, including the bioremediation of contaminated sites. Previous studies have demonstrated that ground-penetrating radar (GPR) can be used to detect the products of microbial activity in the subsurface, such as changes in bulk electrical conductivity, mineral dissolution and precipitation, and the formation of biogenic gas. We present field and laboratory experiments that offer insights to the response of GPR signals to microbial activity. In the field, time-lapse borehole radar tomography was used to monitor biodegradation of a hydrocarbon plume over a period of two years. A dense grid of fourteen borehole pairs monitoring the bioactive region showed radar wave velocity changes of +/-4% and signal attenuation changes of +/-25%. These GPR observations correlated spatially and temporally to independent measurements of groundwater velocity and geochemical variations that occurred in response to microbial activity. The greatest relative changes in radar wave velocity of propagation and attenuation were observed in the region of enhanced bacterial stimulation where biomass growth was the greatest. Radar wave velocity and attenuation decreased during periods of enhanced biostimulation. Two laboratory experiments were conducted to further assess radar response to biomass growth. The first experiment monitored GPR wave transmission through a water-saturated quartz-sand reactor during the course of enhanced biostimulation. Radar wave velocity initially decreased as a result of bacterial activity and subsequently increased rapidly as biogenic gas formed in the pore space. Radar signal attenuation increased during the course of the experiment as a result of an

  11. Development of Multiscale Biological Image Data Analysis: Review of 2006 International Workshop on Multiscale Biological Imaging, Data Mining and Informatics, Santa Barbara, USA (BII06)

    OpenAIRE

    Auer, Manfred; Peng, Hanchuan; Singh, Ambuj

    2007-01-01

    The 2006 International Workshop on Multiscale Biological Imaging, Data Mining and Informatics was held at Santa Barbara, on Sept 7–8, 2006. Based on the presentations at the workshop, we selected and compiled this collection of research articles related to novel algorithms and enabling techniques for bio- and biomedical image analysis, mining, visualization, and biology applications.

  12. Fusion Core Imaging Experiment Based on the Shenguang Ⅱ Facility

    Institute of Scientific and Technical Information of China (English)

    郑志坚; 曹磊峰; 滕浩; 成金秀

    2002-01-01

    A laser fusion experiment was performed based on the Shenguang Ⅱ facility. An image of thermonuclear burning region was obtained with a Fresnel zone plate-coded imaging technique, where the laser-driven target was served as an α-particle source, and the coded image obtained in the experiment was reconstructed by a numerical way.

  13. Lessons learned about spaceflight and cell biology experiments

    Science.gov (United States)

    Hughes-Fulford, Millie

    2004-01-01

    Conducting cell biology experiments in microgravity can be among the most technically challenging events in a biologist's life. Conflicting events of spaceflight include waiting to get manifested, delays in manifest schedules, training astronauts to not shake your cultures and to add reagents slowly, as shaking or quick injection can activate signaling cascades and give you erroneous results. It is important to select good hardware that is reliable. Possible conflicting environments in flight include g-force and vibration of launch, exposure of cells to microgravity for extended periods until hardware is turned on, changes in cabin gases and cosmic radiation. One should have an on-board 1-g control centrifuge in order to eliminate environmental differences. Other obstacles include getting your funding in a timely manner (it is not uncommon for two to three years to pass between notification of grant approval for funding and actually getting funded). That said, it is important to note that microgravity research is worthwhile since all terrestrial life evolved in a gravity field and secrets of biological function may only be answered by removing the constant of gravity. Finally, spaceflight experiments are rewarding and worth your effort and patience.

  14. Lessons learned about spaceflight and cell biology experiments

    Science.gov (United States)

    Hughes-Fulford, Millie

    2004-01-01

    Conducting cell biology experiments in microgravity can be among the most technically challenging events in a biologist's life. Conflicting events of spaceflight include waiting to get manifested, delays in manifest schedules, training astronauts to not shake your cultures and to add reagents slowly, as shaking or quick injection can activate signaling cascades and give you erroneous results. It is important to select good hardware that is reliable. Possible conflicting environments in flight include g-force and vibration of launch, exposure of cells to microgravity for extended periods until hardware is turned on, changes in cabin gases and cosmic radiation. One should have an on-board 1-g control centrifuge in order to eliminate environmental differences. Other obstacles include getting your funding in a timely manner (it is not uncommon for two to three years to pass between notification of grant approval for funding and actually getting funded). That said, it is important to note that microgravity research is worthwhile since all terrestrial life evolved in a gravity field and secrets of biological function may only be answered by removing the constant of gravity. Finally, spaceflight experiments are rewarding and worth your effort and patience.

  15. Influencing attitudes toward science through field experiences in biology

    Science.gov (United States)

    Carpenter, Deborah Mcintyre

    The purpose of this study was to determine how student attitudes toward science are influenced by field experiences in undergraduate biology courses. The study was conducted using two institutions of higher education including a 2-year lower-level and a 2-year upper-level institution. Data were collected through interviews with student participants, focus group discussions, students' journal entries, and field notes recorded by the researcher during the field activities. Photographs and video recordings were also used as documentation sources. Data were collected over a period of 34 weeks. Themes that emerged from the qualitative data included students' beliefs that field experiences (a) positively influence student motivation to learn, (b) increase student ability to learn the concepts being taught, and (c) provide opportunities for building relationships and for personal growth. The findings of the study reinforce the importance of offering field-study programs at the undergraduate level to allow undergraduate students the opportunity to experience science activities in a field setting. The research study was framed by the behavioral and developmental theories of attitude and experience including the Theory of Planned Behavior (Ajzen, 1991) and the Theory of Experiential Learning (Kolb, 1984).

  16. Organising multi-dimensional biological image information: the BioImage Database.

    Science.gov (United States)

    Carazo, J M; Stelzer, E H; Engel, A; Fita, I; Henn, C; Machtynger, J; McNeil, P; Shotton, D M; Chagoyen, M; de Alarcón, P A; Fritsch, R; Heymann, J B; Kalko, S; Pittet, J J; Rodriguez-Tomé, P; Boudier, T

    1999-01-01

    Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. At the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on BioImage started two years ago, and that its first version is now presented here. In essence, BioImage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of BioImage can be accessed at http://www. bioimage.org and http://www-embl.bioimage.org

  17. Biological Tissue Imaging with a Position and Time Sensitive Pixelated Detector

    CERN Document Server

    Jungmann, Julia H; MacAleese, Luke; Klinkert, Ivo; Visser, Jan; Heeren, Ron M A

    2013-01-01

    We demonstrate the capabilities of a highly parallel, active pixel detector for large-area, mass spectrometric imaging of biological tissue sections. A bare Timepix assembly (512x512 pixels) is combined with chevron microchannel plates on an ion microscope matrix-assisted laser desorption time-of-flight mass spectrometer (MALDI TOF-MS). The detector assembly registers position- and time-resolved images of multiple m/z species in every measurement frame. We prove the applicability of the detection system to bio-molecular mass spectrometry imaging on biologically relevant samples by mass-resolved images from Timepix measurements of a peptide-grid benchmark sample and mouse testis tissue slices. Mass-spectral and localization information of analytes at physiological concentrations are measured in MALDI-TOF-MS imaging experiments. We show a high spatial resolution (pixel size down to 740x740 nm2 on the sample surface) and a spatial resolving power of 6 {\\mu}m with a microscope mode laser field of view of 100-335 ...

  18. THE Q/U IMAGING EXPERIMENT INSTRUMENT

    Energy Technology Data Exchange (ETDEWEB)

    Bischoff, C.; Brizius, A.; Buder, I.; Kusaka, A.; Smith, K. M.; Bogdan, M. [Kavli Institute for Cosmological Physics, Department of Physics, Enrico Fermi Institute, The University of Chicago, Chicago, IL 60637 (United States); Chinone, Y. [High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Cleary, K.; Reeves, R. [Cahill Center for Astronomy and Astrophysics, California Institute of Technology, 1200 E. California Blvd M/C 249-17, Pasadena, CA 91125 (United States); Dumoulin, R. N.; Newburgh, L. B. [Department of Physics and Columbia Astrophysics Laboratory, Columbia University, New York, NY 10027 (United States); Monsalve, R.; Bustos, R. [Department of Physics, University of Miami, 1320 Campo Sano Drive, Coral Gables, FL 33146 (United States); Naess, S. K. [Institute of Theoretical Astrophysics, University of Oslo, P.O. Box 1029 Blindern, N-0315 Oslo (Norway); Nixon, G. [Joseph Henry Laboratories of Physics, Jadwin Hall, Princeton University, Princeton, NJ 08544 (United States); Vanderlinde, K. [Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8 (Canada); Wehus, I. K. [Department of Physics, University of Oslo, P.O. Box 1048 Blindern, N-0316 Oslo (Norway); Church, S. E. [Kavli Institute for Particle Astrophysics and Cosmology and Department of Physics, Stanford University, Varian Physics Building, 382 Via Pueblo Mall, Stanford, CA 94305 (United States); Davis, R.; Dickinson, C., E-mail: newburgh@princeton.edu [Jodrell Bank Centre for Astrophysics, Alan Turing Building, School of Physics and Astronomy, University of Manchester, Oxford Road, Manchester M13 9PL (United Kingdom); and others

    2013-05-01

    The Q/U Imaging ExperimenT (QUIET) is designed to measure polarization in the cosmic microwave background, targeting the imprint of inflationary gravitational waves at large angular scales({approx}1 Degree-Sign ). Between 2008 October and 2010 December, two independent receiver arrays were deployed sequentially on a 1.4 m side-fed Dragonian telescope. The polarimeters that form the focal planes use a compact design based on high electron mobility transistors (HEMTs) that provides simultaneous measurements of the Stokes parameters Q, U, and I in a single module. The 17-element Q-band polarimeter array, with a central frequency of 43.1 GHz, has the best sensitivity (69 {mu}Ks{sup 1/2}) and the lowest instrumental systematic errors ever achieved in this band, contributing to the tensor-to-scalar ratio at r < 0.1. The 84-element W-band polarimeter array has a sensitivity of 87 {mu}Ks{sup 1/2} at a central frequency of 94.5 GHz. It has the lowest systematic errors to date, contributing at r < 0.01. The two arrays together cover multipoles in the range l {approx} 25-975. These are the largest HEMT-based arrays deployed to date. This article describes the design, calibration, performance, and sources of systematic error of the instrument.

  19. Troubleshooting digital macro photography for image acquisition and the analysis of biological samples.

    Science.gov (United States)

    Liepinsh, Edgars; Kuka, Janis; Dambrova, Maija

    2013-01-01

    For years, image acquisition and analysis have been an important part of life science experiments to ensure the adequate and reliable presentation of research results. Since the development of digital photography and digital planimetric methods for image analysis approximately 20 years ago, new equipment and technologies have emerged, which have increased the quality of image acquisition and analysis. Different techniques are available to measure the size of stained tissue samples in experimental animal models of disease; however, the most accurate method is digital macro photography with software that is based on planimetric analysis. In this study, we described the methodology for the preparation of infarcted rat heart and brain tissue samples before image acquisition, digital macro photography techniques and planimetric image analysis. These methods are useful in the macro photography of biological samples and subsequent image analysis. In addition, the techniques that are described in this study include the automated analysis of digital photographs to minimize user input and exclude the risk of researcher-generated errors or bias during image analysis.

  20. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

    Science.gov (United States)

    Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

    2011-12-15

    The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research

  1. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

    Science.gov (United States)

    2011-01-01

    Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from

  2. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

    Directory of Open Access Journals (Sweden)

    Waltemath Dagmar

    2011-12-01

    Full Text Available Abstract Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML. SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s used

  3. Selection Experiments in the Penna Model for Biological Aging

    Science.gov (United States)

    Medeiros, G.; Idiart, M. A.; de Almeida, R. M. C.

    We consider the Penna model for biological aging to investigate correlations between early fertility and late life survival rates in populations at equilibrium. We consider inherited initial reproduction ages together with a reproduction cost translated in a probability that mother and offspring die at birth, depending on the mother age. For convenient sets of parameters, the equilibrated populations present genetic variability in what regards both genetically programmed death age and initial reproduction age. In the asexual Penna model, a negative correlation between early life fertility and late life survival rates naturally emerges in the stationary solutions. In the sexual Penna model, selection experiments are performed where individuals are sorted by initial reproduction age from the equilibrated populations and the separated populations are evolved independently. After a transient, a negative correlation between early fertility and late age survival rates also emerges in the sense that populations that start reproducing earlier present smaller average genetically programmed death age. These effects appear due to the age structure of populations in the steady state solution of the evolution equations. We claim that the same demographic effects may be playing an important role in selection experiments in the laboratory.

  4. Real time endoscopic and functional imaging of biological ultrastructure using optical coherence tomography

    Science.gov (United States)

    Rollins, Andrew Martin

    2000-10-01

    Optical coherence tomography (OCT) is a relatively new, non-invasive optical imaging technique. OCT is well suited to in situ imaging of biological ultrastructure, providing micron-scale resolution in three dimensions to a depth of a few millimeters without contacting the tissue. The objective of this research was to advance the state of the art in OCT imaging in order to enable endoscopic examination of gastrointestinal mucosae, and to explore functional imaging extensions to the technology. We present a high speed OCT system capable of imaging in real time. Issues critical to real time OCT imaging are discussed, with an emphasis on rapid scanning optical delay lines, and real time signal conditioning, acquisition, and display instrumentation. Results of experiments demonstrating real time OCT imaging are presented, including in vivo samples. The real time OCT system was integrated with a custom catheter probe in a prototype endoscopic OCT (EOCT) unit appropriate for clinical studies. We report on the design and initial clinical experience with the real-time EOCT imaging system. Results of initial clinical studies are presented. EOCT imaging clearly delineates the substructure of the mucosa and submucosa in several gastrointestinal organs. Color Doppler optical coherence tomography (CDOCT) is a functional extension of OCT that can image flow in turbid media with micron-scale spatial resolution. We present a real-time CDOCT system that is capable of imaging flow at high frame rates. Imaging of flow in tissue simulating phantom and in vivo in an animal model is demonstrated. Further, we introduce a family of power-conserving fiber- optic interferometer designs for OCT. Simple design equations for optimization of the signal to noise ratio of the interferometers are expressed in terms of relevant signal and noise sources and measurable system parameters. Finally, we discuss a number of future directions for OCT research. The spectroscopic OCT techniques of wavelength

  5. Experiences with digital processing of images at INPE

    Science.gov (United States)

    Mascarenhas, N. D. A. (Principal Investigator)

    1984-01-01

    Four different research experiments with digital image processing at INPE will be described: (1) edge detection by hypothesis testing; (2) image interpolation by finite impulse response filters; (3) spatial feature extraction methods in multispectral classification; and (4) translational image registration by sequential tests of hypotheses.

  6. Using biologically interrelated experiments to identify pathway genes in Arabidopsis

    OpenAIRE

    Kim, Kyungpil; Jiang, Keni; Teng, Siew Leng; Feldman, Lewis J.; Huang, Haiyan

    2012-01-01

    Motivation: Pathway genes are considered as a group of genes that work cooperatively in the same pathway constituting a fundamental functional grouping in a biological process. Identifying pathway genes has been one of the major tasks in understanding biological processes. However, due to the difficulty in characterizing/inferring different types of biological gene relationships, as well as several computational issues arising from dealing with high-dimensional biological data, deducing ge...

  7. Imaging of Biological Materials and Cells by X-ray Scattering and Diffraction.

    Science.gov (United States)

    Hémonnot, Clément Y J; Köster, Sarah

    2017-09-26

    Cells and biological materials are large objects in comparison to the size of internal components such as organelles and proteins. An understanding of the functions of these nanoscale elements is key to elucidating cellular function. In this review, we describe the advances in X-ray scattering and diffraction techniques for imaging biological systems at the nanoscale. We present a number of principal technological advances in X-ray optics and development of sample environments. We identify radiation damage as one of the most severe challenges in the field, thus rendering the dose an important parameter when putting different X-ray methods in perspective. Furthermore, we describe different successful approaches, including scanning and full-field techniques, along with prominent examples. Finally, we present a few recent studies that combined several techniques in one experiment in order to collect highly complementary data for a multidimensional sample characterization.

  8. ISPA (imaging silicon pixel array) experiment

    CERN Multimedia

    Patrice Loïez

    2002-01-01

    Application components of ISPA tubes are shown: the CERN-developed anode chip, special windows for gamma and x-ray detection, scintillating crystal and fibre arrays for imaging and tracking of ionizing particles.

  9. Strain-sensitive upconversion for imaging biological forces (Conference Presentation)

    Science.gov (United States)

    Lay, Alice; Wisser, Michael; Lin, Yu; Narayan, Tarun; Krieg, Michael; Atre, Ashwin; Goodman, Miriam; Dionne, Jennifer A.

    2016-09-01

    Nearly all diseases can be traced back to abnormal mechanotransduction, but few sensors can reliably measure biologically-relevant forces in vivo. Here, we investigate sub-25nm lanthanide-doped upconverting nanoparticles as novel optical force probes, which provide several biocompatible features: sharp emission peaks with near infrared illumination, a high signal-to-noise ratio, and photostability. To increase force sensitivity, we include d-metal doping in the nanoparticles; the d-metal siphons energy from the lanthanide ions with an efficiency that varies with pressure. We synthesize cubic-phase NaYF4: Er3+,Yb3+ nanoparticles doped with 0-5% Mn2+ and compress them in a hydrostatic environment using a diamond anvil cell. When illuminated at 980nm, the nanoparticles show sharp emission peaks centered at wavelengths of 522nm, 545nm, and 660nm. In 20nN increments, up to 700nN, the ratio of the red-to-green peaks in 0% Mn-doped nanoparticles increases by nearly 30%, resulting in a perceived color change from orange to red. In contrast, the 1% Mn-doped samples exhibit little color change but a large 40% decrease in upconversion intensity. In both cases, the red-to-green ratio varies linearly with strain and the optical properties are recoverable upon release. We further use atomic force microscopy to characterize optical responses at lower, pico-Newton to nano-Newton forces. To demonstrate in vivo imaging capabilities, we incubate C. elegans with nanoparticles dispersed in buffer solution (5mg/mL concentration) and image forces involved in digestion using confocal microscopy. Our nanoparticles provide a platform for the first, non-genetically-encoded in vivo force sensors, and we describe routes to increase their sensitivity to the single-pN range.

  10. Cell Wall Biology: Perspectives from Cell Wall Imaging

    Institute of Scientific and Technical Information of China (English)

    Kieran J.D.Lee; Susan E.Marcus; J.Paul Knox

    2011-01-01

    Polysaccharide-rich plant cell walls are important biomaterials that underpin plant growth,are major repositories for photosynthetically accumulated carbon,and,in addition,impact greatly on the human use of plants. Land plant cell walls contain in the region of a dozen major polysaccharide structures that are mostly encompassed by cellulose,hemicelluloses,and pectic polysaccharides. During the evolution of land plants,polysaccharide diversification appears to have largely involved structural elaboration and diversification within these polysaccharide groups. Cell wall chemistry is well advanced and a current phase of cell wall science is aimed at placing the complex polysaccharide chemistry in cellular contexts and developing a detailed understanding of cell wall biology. Imaging cell wall glycomes is a challenging area but recent developments in the establishment of cell wall molecular probe panels and their use in high throughput procedures are leading to rapid advances in the molecular understanding of the spatial heterogeneity of individual cell walls and also cell wall differences at taxonomic levels. The challenge now is to integrate this knowledge of cell wall heterogeneity with an understanding of the molecular and physiological mechanisms that underpin cell wall properties and functions.

  11. A Practical Approach to Quantitative Processing and Analysis of Small Biological Structures by Fluorescent Imaging

    Science.gov (United States)

    Noller, Crystal M.; Boulina, Maria; McNamara, George; Szeto, Angela; McCabe, Philip M.

    2016-01-01

    Standards in quantitative fluorescent imaging are vaguely recognized and receive insufficient discussion. A common best practice is to acquire images at Nyquist rate, where highest signal frequency is assumed to be the highest obtainable resolution of the imaging system. However, this particular standard is set to insure that all obtainable information is being collected. The objective of the current study was to demonstrate that for quantification purposes, these correctly set acquisition rates can be redundant; instead, linear size of the objects of interest can be used to calculate sufficient information density in the image. We describe optimized image acquisition parameters and unbiased methods for processing and quantification of medium-size cellular structures. Sections of rabbit aortas were immunohistochemically stained to identify and quantify sympathetic varicosities, >2 μm in diameter. Images were processed to reduce background noise and segment objects using free, open-access software. Calculations of the optimal sampling rate for the experiment were based on the size of the objects of interest. The effect of differing sampling rates and processing techniques on object quantification was demonstrated. Oversampling led to a substantial increase in file size, whereas undersampling hindered reliable quantification. Quantification of raw and incorrectly processed images generated false structures, misrepresenting the underlying data. The current study emphasizes the importance of defining image-acquisition parameters based on the structure(s) of interest. The proposed postacquisition processing steps effectively removed background and noise, allowed for reliable quantification, and eliminated user bias. This customizable, reliable method for background subtraction and structure quantification provides a reproducible tool for researchers across biologic disciplines. PMID:27182204

  12. ISPA (imaging silicon pixel array) experiment

    CERN Multimedia

    Patrice Loïez

    2002-01-01

    On the table, under the scrutiny of some collaboration members, an ISPA tube (upper-left of the table) with some of its application components is shown: they consist of the CERN-developed anode chip, special windows for gamma and x-ray detection, scintillating crystal and fibre arrays for imaging and tracking of ionizing particles.

  13. Application of shift-and-add algorithms for imaging objects within biological media

    Science.gov (United States)

    Aizert, Avishai; Moshe, Tomer; Abookasis, David

    2017-01-01

    The Shift-and-Add (SAA) technique is a simple mathematical operation developed to reconstruct, at high spatial resolution, atmospherically degraded solar images obtained from stellar speckle interferometry systems. This method shifts and assembles individual degraded short-exposure images into a single average image with significantly improved contrast and detail. Since the inhomogeneous refractive indices of biological tissue causes light scattering similar to that induced by optical turbulence in the atmospheric layers, we assume that SAA methods can be successfully implemented to reconstruct the image of an object within a scattering biological medium. To test this hypothesis, five SAA algorithms were evaluated for reconstructing images acquired from multiple viewpoints. After successfully retrieving the hidden object's shape, quantitative image quality metrics were derived, enabling comparison of imaging error across a spectrum of layer thicknesses, demonstrating the relative efficacy of each SAA algorithm for biological imaging.

  14. Functionalized nanoparticles for biological imaging and detection applications

    Science.gov (United States)

    Mei, Bing C.

    Semiconductor quantum dots (QDs) and gold nanoparticles (AuNPs) have gained tremendous attention in the last decade as a result of their size-dependent spectroscopic properties. These nanoparticles have been a subject of intense study to bridge the gap between macroscopic and atomic behavior, as well as to generate new materials for novel applications in therapeutics, biological sensing, light emitting devices, microelectronics, lasers, and solar cells. One of the most promising areas for the use of these nanoparticles is in biotechnology, where their size-dependent optical properties are harnessed for imaging and sensing applications. However, these nanoparticles, as synthesized, are often not stable in aqueous media and lack simple and reliable means of covalently linking to biomolecules. The focus of this work is to advance the progress of these nanomaterials for biotechnology by synthesizing them, characterizing their optical properties and rendering them water-soluble and functional while maintaining their coveted optical properties. QDs were synthesized by an organometallic chemical procedure that utilizes coordinating solvents to provide brightly luminescent nanoparticles. The optical interactions of these QDs were studied as a function of concentration to identify particle size-dependent optimal concentrations, where scattering and indirection excitation are minimized and the amount light observed per particle is maximized. Both QDs and AuNPs were rendered water-soluble and stable in a broad range of biologically relevant conditions by using a series of ligands composed of dihydrolipoic acid (DHLA) appended to poly(ethylene glycol) methyl ether. By studying the stability of the surface modified AuNPs, we revealed some interesting information regarding the role of the surface ligand on the nanoparticle stability (i.e. solubility in high salt concentration, resistance to dithiothreitol competition and cyanide decomposition). Furthermore, the nanoparticles

  15. Single-molecule experiments in biological physics: methods and applications.

    Science.gov (United States)

    Ritort, F

    2006-08-16

    I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

  16. Development of Two Color Fluorescent Imager and Integrated Fluidic System for Nanosatellite Biology Applications

    Science.gov (United States)

    Wu, Diana Terri; Ricco, Antonio Joseph; Lera, Matthew P.; Timucin, Linda R.; Parra, Macarena P.

    2012-01-01

    Nanosatellites offer frequent, low-cost space access as secondary payloads on launches of larger conventional satellites. We summarize the payload science and technology of the Microsatellite in-situ Space Technologies (MisST) nanosatellite for conducting automated biological experiments. The payload (two fused 10-cm cubes) includes 1) an integrated fluidics system that maintains organism viability and supports growth and 2) a fixed-focus imager with fluorescence and scattered-light imaging capabilities. The payload monitors temperature, pressure and relative humidity, and actively controls temperature. C. elegans (nematode, 50 m diameter x 1 mm long) was selected as a model organism due to previous space science experience, its completely sequenced genome, size, hardiness, and the variety of strains available. Three strains were chosen: two green GFP-tagged strains and one red tdTomato-tagged strain that label intestinal, nerve, and pharyngeal cells, respectively. The integrated fluidics system includes bioanalytical and reservoir modules. The former consists of four 150 L culture wells and a 4x5 mm imaging zone the latter includes two 8 mL fluid reservoirs for reagent and waste storage. The fluidic system is fabricated using multilayer polymer rapid prototyping: laser cutting, precision machining, die cutting, and pressure-sensitive adhesives it also includes eight solenoid-operated valves and one mini peristaltic pump. Young larval-state (L2) nematodes are loaded in C. elegans Maintenance Media (CeMM) in the bioanalytical module during pre-launch assembly. By the time orbit is established, the worms have grown to sufficient density to be imaged and are fed fresh CeMM. The strains are pumped sequentially into the imaging area, imaged, then pumped into waste. Reagent storage utilizes polymer bags under slight pressure to prevent bubble formation in wells or channels. The optical system images green and red fluorescence bands by excitation with blue (473 nm peak

  17. A National Comparison of Biochemistry and Molecular Biology Capstone Experiences

    Science.gov (United States)

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the "American Society for Biochemistry and Molecular Biology" (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end,…

  18. Experience with CANDID: Comparison algorithm for navigating digital image databases

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, P.; Cannon, M.

    1994-10-01

    This paper presents results from the authors experience with CANDID (Comparison Algorithm for Navigating Digital Image Databases), which was designed to facilitate image retrieval by content using a query-by-example methodology. A global signature describing the texture, shape, or color content is first computed for every image stored in a database, and a normalized similarity measure between probability density functions of feature vectors is used to match signatures. This method can be used to retrieve images from a database that are similar to a user-provided example image. Results for three test applications are included.

  19. Mass Spectrometry Imaging of Biological Tissue: An Approach for Multicenter Studies

    Energy Technology Data Exchange (ETDEWEB)

    Rompp, Andreas; Both, Jean-Pierre; Brunelle, Alain; Heeren, Ronald M.; Laprevote, Olivier; Prideaux, Brendan; Seyer, Alexandre; Spengler, Bernhard; Stoeckli, Markus; Smith, Donald F.

    2015-03-01

    Mass spectrometry imaging has become a popular tool for probing the chemical complexity of biological surfaces. This led to the development of a wide range of instrumentation and preparation protocols. It is thus desirable to evaluate and compare the data output from different methodologies and mass spectrometers. Here, we present an approach for the comparison of mass spectrometry imaging data from different laboratories (often referred to as multicenter studies). This is exemplified by the analysis of mouse brain sections in five laboratories in Europe and the USA. The instrumentation includes matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF), MALDI-QTOF, MALDIFourier transform ion cyclotron resonance (FTICR), atmospheric-pressure (AP)-MALDI-Orbitrap, and cluster TOF-secondary ion mass spectrometry (SIMS). Experimental parameters such as measurement speed, imaging bin width, and mass spectrometric parameters are discussed. All datasets were converted to the standard data format imzML and displayed in a common open-source software with identical parameters for visualization, which facilitates direct comparison of MS images. The imzML conversion also allowed exchange of fully functional MS imaging datasets between the different laboratories. The experiments ranged from overview measurements of the full mouse brain to detailed analysis of smaller features (depending on spatial resolution settings), but common histological features such as the corpus callosum were visible in all measurements. High spatial resolution measurements of AP-MALDI-Orbitrap and TOF-SIMS showed comparable structures in the low-micrometer range. We discuss general considerations for planning and performing multicenter studies in mass spectrometry imaging. This includes details on the selection, distribution, and preparation of tissue samples as well as on data handling. Such multicenter studies in combination with ongoing activities for reporting guidelines, a common

  20. Cerenkov Radiation Energy Transfer (CRET) Imaging: A Novel Method for Optical Imaging of PET Isotopes in Biological Systems: e13300

    National Research Council Canada - National Science Library

    Robin S Dothager; Reece J Goiffon; Erin Jackson; Scott Harpstrite; David Piwnica-Worms

    2010-01-01

    .... Principal Findings To improve optical imaging of Cerenkov radiation in biological systems, we demonstrate that Cerenkov radiation from decay of the PET isotopes 64Cu and 18F can be spectrally coupled...

  1. Mammographic quantitative image analysis and biologic image composition for breast lesion characterization and classification

    Energy Technology Data Exchange (ETDEWEB)

    Drukker, Karen, E-mail: kdrukker@uchicago.edu; Giger, Maryellen L.; Li, Hui [Department of Radiology, University of Chicago, Chicago, Illinois 60637 (United States); Duewer, Fred; Malkov, Serghei; Joe, Bonnie; Kerlikowske, Karla; Shepherd, John A. [Radiology Department, University of California, San Francisco, California 94143 (United States); Flowers, Chris I. [Department of Radiology, University of South Florida, Tampa, Florida 33612 (United States); Drukteinis, Jennifer S. [Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612 (United States)

    2014-03-15

    Purpose: To investigate whether biologic image composition of mammographic lesions can improve upon existing mammographic quantitative image analysis (QIA) in estimating the probability of malignancy. Methods: The study population consisted of 45 breast lesions imaged with dual-energy mammography prior to breast biopsy with final diagnosis resulting in 10 invasive ductal carcinomas, 5 ductal carcinomain situ, 11 fibroadenomas, and 19 other benign diagnoses. Analysis was threefold: (1) The raw low-energy mammographic images were analyzed with an established in-house QIA method, “QIA alone,” (2) the three-compartment breast (3CB) composition measure—derived from the dual-energy mammography—of water, lipid, and protein thickness were assessed, “3CB alone”, and (3) information from QIA and 3CB was combined, “QIA + 3CB.” Analysis was initiated from radiologist-indicated lesion centers and was otherwise fully automated. Steps of the QIA and 3CB methods were lesion segmentation, characterization, and subsequent classification for malignancy in leave-one-case-out cross-validation. Performance assessment included box plots, Bland–Altman plots, and Receiver Operating Characteristic (ROC) analysis. Results: The area under the ROC curve (AUC) for distinguishing between benign and malignant lesions (invasive and DCIS) was 0.81 (standard error 0.07) for the “QIA alone” method, 0.72 (0.07) for “3CB alone” method, and 0.86 (0.04) for “QIA+3CB” combined. The difference in AUC was 0.043 between “QIA + 3CB” and “QIA alone” but failed to reach statistical significance (95% confidence interval [–0.17 to + 0.26]). Conclusions: In this pilot study analyzing the new 3CB imaging modality, knowledge of the composition of breast lesions and their periphery appeared additive in combination with existing mammographic QIA methods for the distinction between different benign and malignant lesion types.

  2. RGB-NIR color image fusion: metric and psychophysical experiments

    Science.gov (United States)

    Hayes, Alex E.; Finlayson, Graham D.; Montagna, Roberto

    2015-01-01

    In this paper, we compare four methods of fusing visible RGB and near-infrared (NIR) images to produce a color output image, using a psychophysical experiment and image fusion quality metrics. The results of the psychophysical experiment show that two methods are significantly preferred to the original RGB image, and therefore RGB-NIR image fusion may be useful for photographic enhancement in those cases. The Spectral Edge method is the most preferred method, followed by the dehazing method of Schaul et al. We then investigate image fusion metrics which give results correlated with the psychophysical experiment results. We extend several existing metrics from 2 to 1 to M to N channel image fusion, as well as introducing new metrics based on output image colorfulness and contrast, and test them on our experimental data. While none of the individual metrics gives a ranking of the algorithms which exactly matches that of the psychophysical experiment, through a combination of two metrics we accurately rank the two leading fusion methods.

  3. Photoactive molecules for applications in molecular imaging and cell biology.

    Science.gov (United States)

    Shao, Qing; Xing, Bengang

    2010-08-01

    Photoactive technology has proven successful for non-invasive regulation of biological activities and processes in living cells. With the light-directed generation of biomaterials or signals, mechanisms in cell biology can be investigated at the molecular level with spatial and temporal resolution. In this tutorial review, we aim to introduce the important applications of photoactive molecules for elucidating cell biology on aspects of protein engineering, fluorescence labelling, gene regulation and cell physiological functions.

  4. ISPA (imaging silicon pixel array) experiment

    CERN Multimedia

    Patrice Loïez

    2002-01-01

    The ISPA tube is a position-sensitive photon detector. It belongs to the family of hybrid photon detectors (HPD), recently developed by CERN and INFN with leading photodetector firms. HPDs confront in a vacuum envelope a photocathode and a silicon detector. This can be a single diode or a pixelized detector. The electrons generated by the photocathode are efficiently detected by the silicon anode by applying a high-voltage difference between them. ISPA tube can be used in high-energy applications as well as bio-medical and imaging applications.

  5. High Mass Accuracy and High Mass Resolving Power FT-ICR Secondary Ion Mass Spectrometry for Biological Tissue Imaging

    CERN Document Server

    Smith, Donald F; Leach, Franklin E; Robinson, Errol W; Paša-Tolić, Ljiljana; Heeren, Ron M A

    2013-01-01

    Biological tissue imaging by secondary ion mass spectrometry has seen rapid development with the commercial availability of polyatomic primary ion sources. Endogenous lipids and other small bio-molecules can now be routinely mapped on the sub-micrometer scale. Such experiments are typically performed on time-of-flight mass spectrometers for high sensitivity and high repetition rate imaging. However, such mass analyzers lack the mass resolving power to ensure separation of isobaric ions and the mass accuracy for elemental formula assignment based on exact mass measurement. We have recently reported a secondary ion mass spectrometer with the combination of a C60 primary ion gun with a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for high mass resolving power, high mass measurement accuracy and tandem mass spectrometry capabilities. In this work, high specificity and high sensitivity secondary ion FT-ICR MS was applied to chemical imaging of biological tissue. An entire rat brain tissu...

  6. A Biochemistry and Molecular Biology Experiment and Evaluation System for Biotechnology Specialty Students: An Effective Evaluation System to Improve the Biochemistry and Molecular Biology Experiment Teaching

    Science.gov (United States)

    Li, Suxia; Wu, Haizhen; Zhao, Jian; Ou, Ling; Zhang, Yuanxing

    2010-01-01

    In an effort to achieve high success in knowledge and technique acquisition as a whole, a biochemistry and molecular biology experiment was established for high-grade biotechnology specialty students after they had studied essential theory and received proper technique training. The experiment was based on cloning and expression of alkaline…

  7. From image quality to atmosphere experience: how evolutions in technology impact experience assessment

    Science.gov (United States)

    Heynderickx, Ingrid; de Ridder, Huib

    2013-03-01

    Image quality is a concept that for long very well served to optimize display performance and signal quality. New technological developments, however, forced the community to look into higher-level concepts to capture the full experience. Terms as naturalness and viewing experience were used to optimize the full experience of 3D-displays and Ambilight TV. These higher-level concepts capture differences in image quality and differences in perceived depth or perceived viewing field. With the introduction of solid-state lighting, further enhancing the multimedia experience, yet more advanced quality evaluation concepts to optimize the overall experience will be needed in the future.

  8. Photoacoustic imaging in both soft and hard biological tissue

    Energy Technology Data Exchange (ETDEWEB)

    Li, T; Dewhurst, R J, E-mail: richard.dewhurst@manchester.ac.u [Photon Science Institute, University of Manchester, Alan Turing Building, Oxford road, Manchester, M13 9PL (United Kingdom)

    2010-03-01

    To date, most Photoacoustic (PA) imaging results have been from soft biotissues. In this study, a PA imaging system with a near-infrared pulsed laser source has been applied to obtain 2-D and 3-D images from both soft tissue and post-mortem dental samples. Imaging results showed that the PA technique has the potential to image human oral disease, such as early-stage teeth decay. For non-invasive photoacoustic imaging, the induced temperature and pressure rises within biotissues should not cause physical damage to the tissue. Several simulations based on the thermoelastic effect have been applied to predict initial temperature and pressure fields within a tooth sample. Predicted initial temperature and pressure rises are below corresponding safety limits.

  9. Multiphoton imaging of biological samples during freezing and heating

    Science.gov (United States)

    Breunig, H. G.; Uchugonova, A.; König, K.

    2014-02-01

    We applied multiphoton microscopic imaging to observe freezing and heating effects in plant- and animal cell samples. The experimental setups consisted of a multiphoton imaging system and a heating and cooling stage which allows for precise temperature control from liquid nitrogen temperature (-196°C 77 K) up to +600°C (873 K) with heating/freezing rates between 0.01 K/min and 150 K/min. Two multiphoton imaging systems were used: a system based on a modified optical microscope and a flexible mobile system. To illustrate the imaging capabilities, plant leafs as well as animal cells were microscopically imaged in vivo during freezing based on autofluorescence lifetime and intensity of intrinsic molecules. The measurements illustrate the usefulness of multiphoton imaging to investigate freezing effects on animal and plant cells.

  10. Can Climate Change Enhance Biology Lessons? A Quasi-Experiment

    Science.gov (United States)

    Monroe, Martha C.; Hall, Stephanie; Li, Christine Jie

    2016-01-01

    Climate change is a highly charged topic that some adults prefer to ignore. If the same holds true for secondary students, teachers could be challenged to teach about climate change. We structured one activity about the biological concepts of carbon cycle and carbon sequestration in two ways: with and without mention of climate change. Results…

  11. Learning Experiences of University Biology Faculty: A Qualitative Pilot Study

    Science.gov (United States)

    Kusch, Jennifer

    2016-01-01

    The study described in this article incorporates qualitative research through in-depth, individual, structured interviews with 12 biology faculty from two Midwestern universities to explore perceptions about how they have learned to teach and how they work to improve their skills.

  12. Birefringence imaging of biological tissue by spectral domain polarization sensitive optical coherence tomography

    Science.gov (United States)

    Jing, Zhijun; Fan, Chuanmao; Jiang, Jingying; Gong, Qiang; Ma, Zhenhe; Zhang, Fan; Yao, Jianquan; Wang, R. K.

    2007-02-01

    A spectral domain Polarization sensitive optical coherence tomography (SDPS-OCT) system has been developed to acquire depth images of biological tissues such as porcine tendon, rabbit eye. The Stocks vectors (I, Q, U, and V) of the backscattered light from the biological tissues have been reconstructed. Further, the phase retardation and polarization degree between the two orthogonal polarizing states have been computed. Reconstructed images, i.e. birefringence images, from Stokes parameters, retardation and polarization degree of biological tissues show significant local variations in the polarization state. And the birefringence contrast of biological tissue possibly changes by some outside force. In addition, the local thickness of the birefringence layer determined with our system is significant. The results presented show SDPS-OCT is a potentially powerful technique to investigate tissue structural properties on the basis of the fact that any fibrous structure with biological tissues can influence the polarization state of light.

  13. Complex fluids in biological systems experiment, theory, and computation

    CERN Document Server

    2015-01-01

    This book serves as an introduction to the continuum mechanics and mathematical modeling of complex fluids in living systems. The form and function of living systems are intimately tied to the nature of surrounding fluid environments, which commonly exhibit nonlinear and history dependent responses to forces and displacements. With ever-increasing capabilities in the visualization and manipulation of biological systems, research on the fundamental phenomena, models, measurements, and analysis of complex fluids has taken a number of exciting directions. In this book, many of the world’s foremost experts explore key topics such as: Macro- and micro-rheological techniques for measuring the material properties of complex biofluids and the subtleties of data interpretation Experimental observations and rheology of complex biological materials, including mucus, cell membranes, the cytoskeleton, and blood The motility of microorganisms in complex fluids and the dynamics of active suspensions Challenges and solut...

  14. Experiences of mobility for people living with rheumatoid arthritis who are receiving biologic drug therapy: implications for podiatry services.

    Science.gov (United States)

    Sanders, Lucy; Donovan-Hall, Margaret; Borthwick, Alan; Bowen, Catherine J

    2017-01-01

    Despite significant advancements in new treatment modalities for rheumatoid arthritis with biological therapies, foot complications remain a disabling and common feature of the disease. In this study the aim was to explore and describe the personal experiences of people with rheumatoid arthritis in receipt of biologic treatments in a bid to understand the impact of this form of medication on their mobility. An interpretative phenomenological analysis (IPA) was undertaken to explore in depth the individual experience of rheumatoid disease through personal accounts of the patient journey spanning both 'before' and 'after' the instigation of biologic therapy. A purposive sampling strategy was adopted and in-depth semi structured interviews used to facilitate rich, detailed interview data exploring the lived experiences of individuals undertaking biological therapy and the changes to mobility experienced as a result. Thematic analysis was employed with an IPA framework to identify key meanings, and report patterns within the data. Five people with rheumatoid arthritis participated in the study. The mean disease duration was 20.2 years (range: 6 -32) and all were being treated with biologic therapies. Four key themes emerged from the data: 1) Life before biologic treatment, depicted in accounts as a negative experience characterised by painful and disabling symptoms and feelings of hopelessness. 2) Life with biologic treatment, often experienced as a life changing transition, restoring function and mobility and offering renewed hope. 3) Sense of self, in which the impact of rheumatoid disease and the subsequent changes arising from biologic therapy reveal a profound impact on feelings of personal identity both pre and post biologic therapy; an effect of footwear on self-image emerges as a dominant sub theme; 4) Unmet footcare needs were evident in the patient narrative, where the unrelenting if diminished impact of foot pain on mobility was viewed in the context of

  15. Greenhouse gas Laser Imaging Tomography Experiment (GreenLITE)

    Energy Technology Data Exchange (ETDEWEB)

    Dobler, Jeremy [Exelis Inc., Fort Wayne, IN (United States); Zaccheo, T. Scott [Exelis Inc., Fort Wayne, IN (United States); Blume, Nathan [Exelis Inc., Fort Wayne, IN (United States); Pernini, Timothy [Exelis Inc., Fort Wayne, IN (United States); Braun, Michael [Exelis Inc., Fort Wayne, IN (United States); Botos, Christopher [Exelis Inc., Fort Wayne, IN (United States)

    2016-03-31

    This report describes the development and testing of a novel system, the Greenhouse gas Laser Imaging Tomography Experiment (GreenLITE), for Monitoring, Reporting and Verification (MRV) of CO2 at Geological Carbon Storage (GCS) sites. The system consists of a pair of laser based transceivers, a number of retroreflectors, and a set of cloud based data processing, storage and dissemination tools, which enable 2-D mapping of the CO2 in near real time. A system was built, tested locally in New Haven, Indiana, and then deployed to the Zero Emissions Research and Technology (ZERT) facility in Bozeman, MT. Testing at ZERT demonstrated the ability of the GreenLITE system to identify and map small underground leaks, in the presence of other biological sources and with widely varying background concentrations. The system was then ruggedized and tested at the Harris test site in New Haven, IN, during winter time while exposed to temperatures as low as -15 °CºC. Additional testing was conducted using simulated concentration enhancements to validate the 2-D retrieval accuracy. This test resulted in a high confidence in the reconstruction ability to identify sources to tens of meters resolution in this configuration. Finally, the system was deployed for a period of approximately 6 months to an active industrial site, Illinois Basin – Decatur Project (IBDP), where >1M metric tons of CO2 had been injected into an underground sandstone basin. The main objective of this final deployment was to demonstrate autonomous operation over a wide range of environmental conditions with very little human interaction, and to demonstrate the feasibility of the system for long term deployment in a GCS environment.

  16. Visualizing aerosol-particle injection for diffractive-imaging experiments

    CERN Document Server

    Awel, Salah; Eckerskorn, Niko; Wiedorn, Max; Horke, Daniel A; Rode, Andrei V; Küpper, Jochen; Chapman, Henry N

    2015-01-01

    Delivering sub-micrometer particles to an intense x-ray focus is a crucial aspect of single-particle diffractive-imaging experiments at x-ray free-electron lasers. Enabling direct visualization of sub-micrometer aerosol particle streams without interfering with the operation of the particle injector can greatly improve the overall efficiency of single-particle imaging experiments by reducing the amount of time and sample consumed during measurements. We have developed in-situ non-destructive imaging diagnostics to aid real-time particle injector optimization and x-ray/particle-beam alignment, based on laser illumination schemes and fast imaging detectors. Our diagnostics are constructed to provide a non-invasive rapid feedback on injector performance during measurements, and have been demonstrated during diffraction measurements at the FLASH free-electron laser.

  17. Introduction to the special issue on molecular imaging in radiation biology.

    Science.gov (United States)

    Humm, John L; Dewhirst, Mark W; Bhujwalla, Zaver M

    2012-04-01

    Molecular imaging is an evolving science that is concerned with the development of novel imaging probes and biomarkers that can be used to non-invasively image molecular and cellular processes. This special issue approaches molecular imaging in the context of radiation research, focusing on biomarkers and imaging methods that provide measurable signals that can assist in the quantification of radiation-induced effects of living systems at the physical, chemical and biological levels. The potential to image molecular changes in response to a radiation insult opens new and exciting opportunities for a more profound understanding of radiation biology, with the possibility of translation of these techniques to radiotherapy practice. This special issue brings together 14 reviews dedicated to the use of molecular imaging in the field of radiation research. The initial three reviews are introductory overviews of the key molecular imaging modalities: magnetic resonance, nuclear and optical. This is followed by 11 reviews each focusing on a specialist area within the field of radiation research. These include: hypoxia and perfusion, tissue metabolism, normal tissue injury, cell death and viability, receptor targeting and nanotechnology, reporter genes, reactive oxygen species (ROS), and biological dosimetry. Over the preceding decade, molecular imaging brought significant new advances to our understanding of every area of radiation biology. This special issue shows us these advances and points to the vibrant future of our field armed with these new capabilities.

  18. Developing students’ ideas about lens imaging: teaching experiments with an image-based approach

    Science.gov (United States)

    Grusche, Sascha

    2017-07-01

    Lens imaging is a classic topic in physics education. To guide students from their holistic viewpoint to the scientists’ analytic viewpoint, an image-based approach to lens imaging has recently been proposed. To study the effect of the image-based approach on undergraduate students’ ideas, teaching experiments are performed and evaluated using qualitative content analysis. Some of the students’ ideas have not been reported before, namely those related to blurry lens images, and those developed by the proposed teaching approach. To describe learning pathways systematically, a conception-versus-time coordinate system is introduced, specifying how teaching actions help students advance toward a scientific understanding.

  19. A Study of the Probe Effect on the Apparent Image of Biological Atomic Force Microscopy

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The probe effect on the apparent image of biological atomic force microscopy was explored in this study, and the potential of AFM in conformational study of gene related biological processes was illustrated by the specific nanostructural information of a new antitumor drug binding to DNA.

  20. Three-dimensional second-harmonic generation imaging of fibrillar collagen in biological tissues.

    Science.gov (United States)

    Xie, Jiansong; Ferbas, John; Juan, Gloria

    2012-07-01

    Multiphoton-induced second-harmonic generation (SHG) has developed into a very powerful approach for in depth visualization of some biological structures with high specificity. In this unit, we describe the basic principles of three-dimensional SHG microscopy. In addition, we illustrate how SHG imaging can be utilized to assess collagen fibrils in biological tissues. Some technical considerations are also addressed.

  1. The Shuttle Imaging Radar B (SIR-B) experiment report

    Science.gov (United States)

    Cimino, Jo Bea; Holt, Benjamin; Richardson, Annie

    1988-01-01

    The primary objective of the SIR-B experiment was to acquire multiple-incidence-angle radar imagery of a variety of Earth's surfaces to better understand the effects of imaging geometry on radar backscatter. A complementary objective was to map extensive regions of particular interest. Under these broad objectives, many specific scientific experiments were defined by the 43 SIR-B Science Team members, including studies in the area of geology, vegetation, radar penetration, oceanography, image analysis, and calibration technique development. Approximately 20 percent of the planned digital data were collected, meeting 40 percent of the scientific objectives. This report is an overview of the SIR-B experiment and includes the science investigations, hardware design, mission scenario, mission operations, events of the actual missions, astronaut participation, data products (including auxiliary data), calibrations, and a summary of the actual coverage. Also included are several image samples.

  2. Changes in operational procedures to improve spaceflight experiments in plant biology in the European Modular Cultivation System

    Science.gov (United States)

    Kiss, John Z.; Aanes, Gjert; Schiefloe, Mona; Coelho, Liz H. F.; Millar, Katherine D. L.; Edelmann, Richard E.

    2014-03-01

    The microgravity environment aboard orbiting spacecraft has provided a unique laboratory to explore topics in basic plant biology as well as applied research on the use of plants in bioregenerative life support systems. Our group has utilized the European Modular Cultivation System (EMCS) aboard the International Space Station (ISS) to study plant growth, development, tropisms, and gene expression in a series of spaceflight experiments. The most current project performed on the ISS was termed Seedling Growth-1 (SG-1) which builds on the previous TROPI (for tropisms) experiments performed in 2006 and 2010. Major technical and operational changes in SG-1 (launched in March 2013) compared to the TROPI experiments include: (1) improvements in lighting conditions within the EMCS to optimize the environment for phototropism studies, (2) the use of infrared illumination to provide high-quality images of the seedlings, (3) modifications in procedures used in flight to improve the focus and overall quality of the images, and (4) changes in the atmospheric conditions in the EMCS incubator. In SG-1, a novel red-light-based phototropism in roots and hypocotyls of seedlings that was noted in TROPI was confirmed and now can be more precisely characterized based on the improvements in procedures. The lessons learned from sequential experiments in the TROPI hardware provide insights to other researchers developing space experiments in plant biology.

  3. Laser Desorption Postionization for Imaging MS of Biological Material

    OpenAIRE

    Akhmetov, Artem; Moore, Jerry F.; Gasper, Gerald L.; Koin, Peter J.; Hanley, Luke

    2010-01-01

    Vacuum ultraviolet single photon ionization (VUV SPI) is a soft ionization technique that has the potential to address many of the limitations of MALDI for imaging MS. Laser desorption postionization (LDPI) employs VUV SPI for postionization and is experimentally analogous to a MALDI instrument with the addition of a pulsed VUV light source. This review discusses progress in LDPI-MS over the last decade, with an emphasis on imaging MS of bacterial biofilms, analytes whose high salt environmen...

  4. Results from neutron imaging of ICF experiments at NIF

    Science.gov (United States)

    Merrill, F. E.; Danly, C. R.; Fittinghoff, D. N.; Grim, G. P.; Guler, N.; Volegov, P. L.; Wilde, C. H.

    2016-03-01

    In 2011 a neutron imaging diagnostic was commissioned at the National Ignition Facility (NIF). This new system has been used to collect neutron images to measure the size and shape of the burning DT plasma and the surrounding fuel assembly. The imaging technique uses a pinhole neutron aperture placed between the neutron source and a neutron detector. The detection system measures the two-dimensional distribution of neutrons passing through the pinhole. This diagnostic collects two images at two times. The long flight path for this diagnostic, 28 m, results in a chromatic separation of the neutrons, allowing the independently timed images to measure the source distribution for two neutron energies. Typically one image measures the distribution of the 14 MeV neutrons, and the other image measures the distribution of the 6-12 MeV neutrons. The combination of these two images has provided data on the size and shape of the burning plasma within the compressed capsule, as well as a measure of the quantity and spatial distribution of the cold fuel surrounding this core. Images have been collected for the majority of the experiments performed as part of the ignition campaign. Results from this data have been used to estimate a burn-averaged fuel assembly as well as providing performance metrics to gauge progress towards ignition. This data set and our interpretation are presented.

  5. Biologically motivated computationally intensive approaches to image pattern recognition

    NARCIS (Netherlands)

    Petkov, Nikolay

    1995-01-01

    This paper presents some of the research activities of the research group in vision as a grand challenge problem whose solution is estimated to need the power of Tflop/s computers and for which computational methods have yet to be developed. The concerned approaches are biologically motivated, in th

  6. Using image analysis to monitor biological changes in consume fish

    DEFF Research Database (Denmark)

    Dissing, Bjørn Skovlund; Frosch, Stina; Nielsen, Michael Engelbrecht

    2011-01-01

    The quality of fish products is largely defined by the visual appearance of the products. Visual appearance includes measurable parameters such as color and texture. Fat content and distribution as well as deposition of carotenoid pigments such as astaxanthin in muscular and fat tissue are biolog...

  7. Imaging Biological Systems using Dielectric Near-Field Microscopy

    Science.gov (United States)

    Brown, Keith; Issadore, David; Hunt, Tom; Westervelt, Robert

    2007-03-01

    We have developed a dielectric spectrometer for use on biological systems. The spectrum of dielectric response to RF electric fields is analogous to color as an optical response. Measurement of the dielectric spectrum from ˜ 10 kHz to ˜ 3 GHz will reveal information about the structure and conditions of protein solutions, protein crystals and biological tissues. We designed and built a system to test biological samples in a microfluidic chamber mounted on a circuit board. The apparatus measures the RF dielectric spectrum directly, or by analyzing the pulse response in the time domain. We have constructed several versions of the hardware for sensitive capacitive measurements, including two types of capacitive bridges, and a transmission line, incorporating precision electronics and local generation of pulses. A goal is to scale the system down and implement many dielectric spectrometers as an array of pixels on a CMOS chip for dielectric near-field microscopy of biological samples. This work made possible by NSEC NSF grant PHY-0117795 and the NCI MIT-Harvard CCNE.

  8. Mesh-Based Fourier Imaging for Biological and Security Applications

    Science.gov (United States)

    Hayden, Danielle

    Traditional x-ray imaging provides only low contrast from low atomic number materials, like soft tissue, due to the small attenuation variations producing very small intensity changes. Higher contrast can be achieved through phase information. The phase change is obtained from the x-ray refracting in a sample, or phase object, due to the difference in refractive indexes. This causes a small angular deviation from the original path. Phase contrast imaging has not been realized in everyday practice due to the requirement for large spatial coherence width of the x-ray beam which typically requires sources on the order of 10-50 m, the use of a grating technique or synchrotron sources. The grating-based phase imaging method depends upon multiple fine-pitched, expensive gratings and extremely precise alignment. An alternative procedure based on a technique recently demonstrated by Bennett is mesh-based phase imaging that utilizes a single, inexpensive mesh with a coarse pitch. This considerably eases the small spot size source requirement, allowing the use of a 150 micron, micro-focus, tungsten anode source. The mesh-based phase imaging set up used to study biomedical and security screening applications consisted of a 123x123 m stainless steel mesh and a 1200x1600 CCD detector with a pixel size of 22 microns. This mesh based approach allows for near-real-time phase extraction of the first harmonics in the Fourier domain. With the phase information and absorption information (collected at the zeroth harmonic), edge enhanced images of a mouse's skull were optimized and several potentially dangerous liquids and powders were discriminated from water. The mesh-based phase set up resulted in high contrasts, signal-to-noise ratios and good resolution verifying the potential utility of this technique for future biomedical imaging and airport security screening.

  9. The Kosmos-1129 biosatellite. [experiments in biological effects of space flight

    Science.gov (United States)

    Nikitin, S. A.

    1980-01-01

    A number of experiments, designed by participating specialists from several countries, are described. The experiments included studies in biorhythm, stress, body parts, behavior, ontogenesis, and gravitational preference. The biological subjects of the experiments were retrieved immediately after the landing of the satellite and examined in a field laboratory.

  10. Procedures for cryogenic X-ray ptychographic imaging of biological samples

    Science.gov (United States)

    Yusuf, M.; Zhang, F.; Chen, B.; Bhartiya, A.; Cunnea, K.; Wagner, U.; Cacho-Nerin, F.; Schwenke, J.; Robinson, I. K.

    2017-01-01

    Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors’ first ptychographic reconstructions using X-rays.

  11. Procedures for cryogenic X-ray ptychographic imaging of biological samples.

    Science.gov (United States)

    Yusuf, M; Zhang, F; Chen, B; Bhartiya, A; Cunnea, K; Wagner, U; Cacho-Nerin, F; Schwenke, J; Robinson, I K

    2017-03-01

    Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors' first ptychographic reconstructions using X-rays.

  12. Procedures for cryogenic X-ray ptychographic imaging of biological samples

    Directory of Open Access Journals (Sweden)

    M. Yusuf

    2017-03-01

    Full Text Available Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors' first ptychographic reconstructions using X-rays.

  13. X-ray phase contrast imaging of biological specimens with tabletop synchrotron radiation

    CERN Document Server

    Kneip, S; Dollar, F; Bloom, M S; Chvykov, V; Kalintchenko, G; Krushelnick, K; Maksimchuk, A; Mangles, S P D; Matsuoka, T; Najmudin, Z; Palmer, C A J; Schreiber, J; Schumaker, W; Thomas, A G R; Yanovsky, V

    2011-01-01

    Since their discovery in 1896, x-rays have had a profound impact on science, medicine and technology. Here we show that the x-rays from a novel tabletop source of bright coherent synchrotron radiation can be applied to phase contrast imaging of biological specimens, yielding superior image quality and avoiding the need for scarce or expensive conventional sources.

  14. Feature detection in biological tissues using multi-band and narrow-band imaging.

    Science.gov (United States)

    Tamura, Yuki; Mashita, Tomohiro; Kuroda, Yoshihiro; Kiyokawa, Kiyoshi; Takemura, Haruo

    2016-12-01

    In the past decade, augmented reality systems have been expected to support surgical operations by making it possible to view invisible objects that are inside or occluded by the skull, hands, or organs. However, the properties of biological tissues that are non-rigid and featureless require a large number of distributed features to track the movement of tissues in detail. With the goal of increasing the number of feature points in organ tracking, we propose a feature detection using multi-band and narrow-band imaging and a new band selection method. The depth of light penetration into an object depends on the wavelength of light based on optical characteristics. We applied typical feature detectors to detect feature points using three selected bands in a human hand. To consider surgical situations, we applied our method to a chicken liver with a variety of light conditions. Our experimental results revealed that the image of each band exhibited a different distribution of feature points. In addition, the total number of feature points determined by the proposed method exceeded that of the R, G, and B images obtained using a normal camera. The results using a chicken liver with various light sources and intensities also show different distributions with each selected band. We have proposed a feature detection method using multi-band and narrow-band imaging and a band selection method. The results of our experiments confirmed that the proposed method increased the number of distributed feature points. The proposed method was also effective for different light conditions.

  15. Compressive Fluorescence Microscopy for Biological and Hyperspectral Imaging

    CERN Document Server

    Studer, Vincent; Chahid, Makhlad; Moussavi, Hamed; Candes, Emmanuel; Dahan, Maxime

    2012-01-01

    The mathematical theory of compressed sensing (CS) asserts that one can acquire signals from measurements whose rate is much lower than the total bandwidth. Whereas the CS theory is now well developed, challenges concerning hardware implementations of CS-based acquisition devices---especially in optics---have only started being addressed. This paper presents an implementation of compressive sensing in fluorescence microscopy and its applications to biomedical imaging. Our CS microscope combines a dynamic structured wide-field illumination and a fast and sensitive single-point fluorescence detection to enable reconstructions of images of fluorescent beads, cells and tissues with undersampling ratios (between the number of pixels and number of measurements) up to 32. We further demonstrate a hyperspectral mode and record images with 128 spectral channels and undersampling ratios up to 64, illustrating the potential benefits of CS acquisition for higher dimensional signals which typically exhibits extreme redund...

  16. Measurement depth enhancement in terahertz imaging of biological tissues.

    Science.gov (United States)

    Oh, Seung Jae; Kim, Sang-Hoon; Jeong, Kiyoung; Park, Yeonji; Huh, Yong-Min; Son, Joo-Hiuk; Suh, Jin-Suck

    2013-09-09

    We demonstrate the use of a THz penetration-enhancing agent (THz-PEA) to enhance the terahertz (THz) wave penetration depth in tissues. The THz-PEA is a biocompatible material having absorption lower than that of water, and it is easily absorbed into tissues. When using glycerol as a THz-PEA, the peak value of the THz signal which was transmitted through the fresh tissue and reflected by a metal target, was almost doubled compared to that of tissue without glycerol. THz time-of-flight imaging (B-scan) was used to display the sequential glycerol delivery images. Enhancement of the penetration depth was confirmed after an artificial tumor was located below fresh skin. We thus concluded that the THz-PEA technique can potentially be employed to enhance the image contrast of the abnormal lesions below the skin.

  17. Experiences of Judeo-Christian Students in Undergraduate Biology

    Science.gov (United States)

    Barnes, M. Elizabeth; Truong, Jasmine M.; Brownell, Sara E.

    2017-01-01

    A major research thrust in science, technology, engineering, and mathematics (STEM) education is focused on how to retain students as STEM majors. The accumulation of seemingly insignificant negative experiences in STEM classes can, over time, lead STEM students to have a low sense of belonging in their disciplines, and this can lead to lower…

  18. Imaging Primary Lung Cancers in Mice to Study Radiation Biology

    OpenAIRE

    Kirsch, David G.; Grimm, Jan; Guimaraes, Alexander R.; Gregory R Wojtkiewicz; Perez, Bradford A.; Santiago, Philip M.; Anthony, Nikolas K.; Forbes, Thomas; Doppke, Karen; Weissleder, Ralph; Jacks, Tyler

    2009-01-01

    Purpose To image a genetically engineered mouse model of non–small-cell lung cancer with micro–computed tomography (micro-CT) to measure tumor response to radiation therapy. Methods and Materials The Cre-loxP system was used to generate primary lung cancers in mice with mutation in K-ras alone or in combination with p53 mutation. Mice were serially imaged by micro-CT, and tumor volumes were determined. A comparison of tumor volume by micro-CT and tumor histology was performed. Tumor ...

  19. Neutron Imaging at the Oak Ridge National Laboratory: Application to Biological Research

    Energy Technology Data Exchange (ETDEWEB)

    Bilheux, Hassina Z [ORNL; Cekanova, Maria [University of Tennessee, Knoxville (UTK); Bilheux, Jean-Christophe [ORNL; Bailey, William Barton [ORNL; Keener, Wylie S [ORNL; Davis, Larry E [ORNL; Herwig, Kenneth W [ORNL

    2014-01-01

    The Oak Ridge National Laboratory Neutron Sciences Directorate (NScD) has recently installed a neutron imaging beamline at the High Flux Isotope Reactor (HFIR) cold guide hall. The CG-1D beamline supports a broad range of user research spanning from engineering to material research, energy storage, additive manufacturing, vehicle technologies, archaeology, biology, and plant physiology. The beamline performance (spatial resolution, field of view, etc.) and its utilization for biological research are presented. The NScD is also considering a proposal to build the VENUS imaging beamline (beam port 10) at the Spallation Neutron Source (SNS). Unlike CG-1D which provides cold neutrons, VENUS will offer a broad range of neutron wavelengths, from epithermal to cold, and enhanced contrast mechanisms. This new capability will also enable the imaging of thicker biological samples than is currently available at CG-1D. A brief overview of the VENUS capability for biological research is discussed.

  20. Nanostructured materials for biological imaging and chemical sensing

    OpenAIRE

    Yıldırım, Adem

    2014-01-01

    Cataloged from PDF version of thesis. Includes bibliographical references (leaves 116-139). Thesis (Ph. D.): Bilkent University, Materials Science and Nanotechnology Program, İhsan Doğramacı Bilkent University, 2014. In the recent years, the design and synthesis of fluorescent nanoparticles for biological and chemical sensing applications have received considerable attention due to the excellent photostability and emission intensity of fluorescent nanoparticles and the intri...

  1. Non-destructive electron microscopy imaging and analysis of biological samples with graphene coating

    Science.gov (United States)

    Park, Jong Bo; Kim, Yong-Jin; Kim, Seong-Min; Yoo, Je Min; Kim, Youngsoo; Gorbachev, Roman; Barbolina, I. I.; Kim, Sang Jin; Kang, Sangmin; Yoon, Myung-Han; Cho, Sung-Pyo; Novoselov, Konstantin S.; Hong, Byung Hee

    2016-12-01

    In electron microscopy (EM), charging of non-conductive biological samples by focused electron beams hinders their high-resolution imaging. Gold or platinum coatings have been commonly used to prevent such sample charging, but it disables further quantitative and qualitative chemical analyses such as energy dispersive spectroscopy (EDS). Here we report that graphene-coating on biological samples enables non-destructive high-resolution imaging by EM as well as chemical analysis by EDS, utilizing graphene’s transparency to electron beams, high conductivity, outstanding mechanical strength and flexibility. We believe that the graphene-coated imaging and analysis would provide us a new opportunity to explore various biological phenomena unseen before due to the limitation in sample preparation and image resolution, which will broaden our understanding on the life mechanism of various living organisms.

  2. Magnetospheric Atmospheric X-ray Imaging Experiment (MAXIE)

    Science.gov (United States)

    Imhof, W. L.; Voss, H. D.; Mobilia, J.; Datlowe, D. W.; Chinn, V. L.; Hilsenrath, M.; Vondrak, R. R.

    1996-01-01

    This report summarizes the activities sponsored by the Office of Naval Research for the Magnetospheric Atmospheric X-ray Imaging Experiment (MAXIE). The MAXIE instrument was developed as a joint activity of Lockheed, The Aerospace Corporation, and the University of Bergen, Norway. Lockheed was responsible for the overall management of the program, interfacing with the appropriate government agencies, the overall electrical and mechanical design, flight software, environmental testing, spacecraft integration activities, on orbit checkout, and data processing activities. The Magnetospheric Atmospheric X-ray Imaging Experiment (MAXIE), the ONR 401 experiment, is the first in a new class of satellite-borne remote sensing instruments. The primary innovation is the ability to obtain rapid, sequential, images with high sensitivity of the earth's X ray aurora from a low altitude polar orbiting satellite. These images can be used to identify dynamic temporal variations in the three-dimensional (energy and position) distribution of electron precipitation into the atmosphere. MAXIE was launched on the TIROS NOAA-13 satellite on 9 August 1993. The experiment performed well during its turn-on sequence; however, the spacecraft bus failed on 21 August 1993. New spacebased technologies successfully used in MAXIE were mixed-mode ASIC microcircuits, a zero torque scanning system with associated viscoelastic damping, a paraffin stow release mechanism, a parallel integrating PHA processor, a low noise Si(Li) sensor telescope, and an advanced thermal cooling system. MAXIE's on orbit operation, control of penetrating particle backgrounds, and scientific data indicated good overall performance.

  3. CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.

    Science.gov (United States)

    Dao, David; Fraser, Adam N; Hung, Jane; Ljosa, Vebjorn; Singh, Shantanu; Carpenter, Anne E

    2016-10-15

    CellProfiler Analyst allows the exploration and visualization of image-based data, together with the classification of complex biological phenotypes, via an interactive user interface designed for biologists and data scientists. CellProfiler Analyst 2.0, completely rewritten in Python, builds on these features and adds enhanced supervised machine learning capabilities (Classifier), as well as visualization tools to overview an experiment (Plate Viewer and Image Gallery). CellProfiler Analyst 2.0 is free and open source, available at http://www.cellprofiler.org and from GitHub (https://github.com/CellProfiler/CellProfiler-Analyst) under the BSD license. It is available as a packaged application for Mac OS X and Microsoft Windows and can be compiled for Linux. We implemented an automatic build process that supports nightly updates and regular release cycles for the software. anne@broadinstitute.orgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  4. Radiation Information for Designing and Interpreting Biological Experiments Onboard Missions Beyond Low Earth Orbit

    Science.gov (United States)

    Straume, T.; Slaba, T.; Bhattacharya, S.; Braby, L. A.

    2017-01-01

    There is growing interest in flying biological experiments beyond low-Earth orbit (LEO) to measure biological responses potentially relevant to those expected during a human mission to Mars. Such experiments could be payloads onboard precursor missions, including unmanned private-public partnerships, as well as small low-cost spacecraft (satellites) designed specifically for biosentinel type missions. Designing such experiments requires knowledge of the radiation environment and its interactions with both the spacecraft and the experimental payload. Information is provided here that is useful for designing such experiments.

  5. Nanomaterial-based activatable imaging probes: from design to biological applications.

    Science.gov (United States)

    Li, Jingjing; Cheng, Fangfang; Huang, Haiping; Li, Lingling; Zhu, Jun-Jie

    2015-11-07

    Activatable imaging probes as alternatives to "always on" imaging probes have attracted more and more attention due to their improved sensitivity and specificity. They are commonly designed to amplify or boost imaging signals only in response to specific biomolecular recognition or interaction. Thus, the design strategies play a vital role in the fabrication of activatable imaging probes. In this review, we focus on the design mechanisms and biological applications of those nanomaterial-based activatable imaging probes reported in the past five years, benefitting greatly from the good development of nanotechnology. These probes not only include the most studied activatable fluorescence imaging probes, but also cover more activatable MR imaging probes based on nanoparticle contrast agents and activatable photoacoustic imaging probes, providing more bases for clinical translation.

  6. Orientation Determination in Single Particle X-ray Coherent Diffraction Imaging Experiments

    CERN Document Server

    Yefanov, O M

    2013-01-01

    Single particle diffraction imaging experiments at free-electron lasers (FEL) have a great potential for structure determination of reproducible biological specimens that can not be crystallized. One of the challenges in processing the data from such an experiment is to determine correct orientation of each diffraction pattern from samples randomly injected in the FEL beam. We propose an algorithm (see also O. Yefanov et al., Photon Science - HASYLAB Annual Report 2010) that can solve this problem and can be applied to samples from tens of nanometers to microns in size, measured with sub-nanometer resolution in the presence of noise. This is achieved by the simultaneous analysis of a large number of diffraction patterns corresponding to different orientations of the particles. The algorithms efficiency is demonstrated for two biological samples, an artificial protein structure without any symmetry and a virus with icosahedral symmetry. Both structures are few tens of nanometers in size and consist of more tha...

  7. PET/MR imaging of atherosclerosis: initial experience and outlook.

    Science.gov (United States)

    Rischpler, Christoph; Nekolla, Stephan G; Beer, Ambros J

    2013-01-01

    Hybrid scanners such as PET/CT have in the past emerged as a valuable modality in clinical routine as well as an important research tool. Recently, the newly developed fully integrated PET/MR scanners were introduced to the market, raising high expectations especially due to the excellent soft tissue contrast and functional imaging capabilities of MRI. In this issue of the American Journal of Nuclear Medicine and Molecular Imaging, initial experiences using a hybrid PET/MR scanner for carotid artery imaging in a group of patients with increased risk for atherosclerosis are described. This represents a proof-of-principle study, which could stimulate future applications of this powerful modality in atherosclerotic plaque imaging.

  8. High-Speed Coherent Raman Fingerprint Imaging of Biological Tissues

    CERN Document Server

    Camp, Charles H; Heddleston, John M; Hartshorn, Christopher M; Walker, Angela R Hight; Rich, Jeremy N; Lathia, Justin D; Cicerone, Marcus T

    2014-01-01

    We have developed a coherent Raman imaging platform using broadband coherent anti-Stokes Raman scattering (BCARS) that provides an unprecedented combination of speed, sensitivity, and spectral breadth. The system utilizes a unique configuration of laser sources that probes the Raman spectrum over 3,000 cm$^{-1}$ and generates an especially strong response in the typically weak Raman "fingerprint" region through heterodyne amplification of the anti-Stokes photons with a large nonresonant background (NRB) while maintaining high spectral resolution of $<$ 13 cm$^{-1}$. For histology and pathology, this system shows promise in highlighting major tissue components in a non-destructive, label-free manner. We demonstrate high-speed chemical imaging in two- and three-dimensional views of healthy murine liver and pancreas tissues and interfaces between xenograft brain tumors and the surrounding healthy brain matter.

  9. IDEAL: Images Across Domains, Experiments, Algorithms and Learning

    Science.gov (United States)

    Ushizima, Daniela M.; Bale, Hrishikesh A.; Bethel, E. Wes; Ercius, Peter; Helms, Brett A.; Krishnan, Harinarayan; Grinberg, Lea T.; Haranczyk, Maciej; Macdowell, Alastair A.; Odziomek, Katarzyna; Parkinson, Dilworth Y.; Perciano, Talita; Ritchie, Robert O.; Yang, Chao

    2016-09-01

    Research across science domains is increasingly reliant on image-centric data. Software tools are in high demand to uncover relevant, but hidden, information in digital images, such as those coming from faster next generation high-throughput imaging platforms. The challenge is to analyze the data torrent generated by the advanced instruments efficiently, and provide insights such as measurements for decision-making. In this paper, we overview work performed by an interdisciplinary team of computational and materials scientists, aimed at designing software applications and coordinating research efforts connecting (1) emerging algorithms for dealing with large and complex datasets; (2) data analysis methods with emphasis in pattern recognition and machine learning; and (3) advances in evolving computer architectures. Engineering tools around these efforts accelerate the analyses of image-based recordings, improve reusability and reproducibility, scale scientific procedures by reducing time between experiments, increase efficiency, and open opportunities for more users of the imaging facilities. This paper describes our algorithms and software tools, showing results across image scales, demonstrating how our framework plays a role in improving image understanding for quality control of existent materials and discovery of new compounds.

  10. IDEAL: Images Across Domains, Experiments, Algorithms and Learning

    Science.gov (United States)

    Ushizima, Daniela M.; Bale, Hrishikesh A.; Bethel, E. Wes; Ercius, Peter; Helms, Brett A.; Krishnan, Harinarayan; Grinberg, Lea T.; Haranczyk, Maciej; Macdowell, Alastair A.; Odziomek, Katarzyna; Parkinson, Dilworth Y.; Perciano, Talita; Ritchie, Robert O.; Yang, Chao

    2016-11-01

    Research across science domains is increasingly reliant on image-centric data. Software tools are in high demand to uncover relevant, but hidden, information in digital images, such as those coming from faster next generation high-throughput imaging platforms. The challenge is to analyze the data torrent generated by the advanced instruments efficiently, and provide insights such as measurements for decision-making. In this paper, we overview work performed by an interdisciplinary team of computational and materials scientists, aimed at designing software applications and coordinating research efforts connecting (1) emerging algorithms for dealing with large and complex datasets; (2) data analysis methods with emphasis in pattern recognition and machine learning; and (3) advances in evolving computer architectures. Engineering tools around these efforts accelerate the analyses of image-based recordings, improve reusability and reproducibility, scale scientific procedures by reducing time between experiments, increase efficiency, and open opportunities for more users of the imaging facilities. This paper describes our algorithms and software tools, showing results across image scales, demonstrating how our framework plays a role in improving image understanding for quality control of existent materials and discovery of new compounds.

  11. Faster, More Reproducible DESI-MS for Biological Tissue Imaging

    Science.gov (United States)

    Tillner, Jocelyn; Wu, Vincen; Jones, Emrys A.; Pringle, Steven D.; Karancsi, Tamas; Dannhorn, Andreas; Veselkov, Kirill; McKenzie, James S.; Takats, Zoltan

    2017-10-01

    A new, more robust sprayer for desorption electrospray ionization (DESI) mass spectrometry imaging is presented. The main source of variability in DESI is thought to be the uncontrolled variability of various geometric parameters of the sprayer, primarily the position of the solvent capillary, or more specifically, its positioning within the gas capillary or nozzle. If the solvent capillary is off-center, the sprayer becomes asymmetrical, making the geometry difficult to control and compromising reproducibility. If the stiffness, tip quality, and positioning of the capillary are improved, sprayer reproducibility can be improved by an order of magnitude. The quality of the improved sprayer and its potential for high spatial resolution imaging are demonstrated on human colorectal tissue samples by acquisition of images at pixel sizes of 100, 50, and 20 μm, which corresponds to a lateral resolution of 40-60 μm, similar to the best values published in the literature. The high sensitivity of the sprayer also allows combination with a fast scanning quadrupole time-of-flight mass spectrometer. This provides up to 30 times faster DESI acquisition, reducing the overall acquisition time for a 10 mm × 10 mm rat brain sample to approximately 1 h. Although some spectral information is lost with increasing analysis speed, the resulting data can still be used to classify tissue types on the basis of a previously constructed model. This is particularly interesting for clinical applications, where fast, reliable diagnosis is required. [Figure not available: see fulltext.

  12. Animal experiments on biological effects of mineral fibres.

    Science.gov (United States)

    Pott, F

    1980-01-01

    The papers presented in this session are summarized. Although asbestos fibres produce tumours in a number of animal species tested, rats appear to be the most susceptible, in terms of latent period and numbers of tumours produced. The deposition, translocation and clearance of different types of fibres in the lung have been investigated in a number of experiments, and it has been shown that many of them migrate more readily than was previously thought; their penetration into the gut was the object of further investigation. The syncarcinogenicity with asbestos of various substances, such as benzo[a]pyrene, N-nitrosodiethylamine, cigarette smoke or radiation, is described. Experiments on the different carcinogenicities of different fibres are summarized; although it is pointed out that there is much controversy in this area. A hypothesis is presented whereby the carcinogenic potency of a fibre is dependent on various size parameters, based on length, diameter and length:diameter ratio. On the basis of this hypothesis, the carcinogenic potency of short fibres may be weak, but many short fibres may induce a tumour as easily as a few long fibres. Finally, a plea is made for a far greater number of well-defined standard samples of asbestos and man-made mineral fibres than exists at present, since there are currently great difficulties in comparing and interpreting results.

  13. The Open Microscopy Environment: open image informatics for the biological sciences

    Science.gov (United States)

    Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

    2016-07-01

    Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

  14. First Human Experience with Directly Image-able Iodinated Embolization Microbeads.

    Science.gov (United States)

    Levy, Elliot B; Krishnasamy, Venkatesh P; Lewis, Andrew L; Willis, Sean; Macfarlane, Chelsea; Anderson, Victoria; van der Bom, Imramsjah Mj; Radaelli, Alessandro; Dreher, Matthew R; Sharma, Karun V; Negussie, Ayele; Mikhail, Andrew S; Geschwind, Jean-Francois H; Wood, Bradford J

    2016-08-01

    To describe first clinical experience with a directly image-able, inherently radio-opaque microspherical embolic agent for transarterial embolization of liver tumors. LC Bead LUMI™ is a new product based upon sulfonate-modified polyvinyl alcohol hydrogel microbeads with covalently bound iodine (~260 mg I/ml). 70-150 μ LC Bead LUMI™ iodinated microbeads were injected selectively via a 2.8 Fr microcatheter to near complete flow stasis into hepatic arteries in three patients with hepatocellular carcinoma, carcinoid, or neuroendocrine tumor. A custom imaging platform tuned for LC LUMI™ microbead conspicuity using a cone beam CT (CBCT)/angiographic C-arm system (Allura Clarity FD20, Philips) was used along with CBCT embolization treatment planning software (EmboGuide, Philips). LC Bead LUMI™ image-able microbeads were easily delivered and monitored during the procedure using fluoroscopy, single-shot radiography (SSD), digital subtraction angiography (DSA), dual-phase enhanced and unenhanced CBCT, and unenhanced conventional CT obtained 48 h after the procedure. Intra-procedural imaging demonstrated tumor at risk for potential under-treatment, defined as paucity of image-able microbeads within a portion of the tumor which was confirmed at 48 h CT imaging. Fusion of pre- and post-embolization CBCT identified vessels without beads that corresponded to enhancing tumor tissue in the same location on follow-up imaging (48 h post). LC Bead LUMI™ image-able microbeads provide real-time feedback and geographic localization of treatment in real time during treatment. The distribution and density of image-able beads within a tumor need further evaluation as an additional endpoint for embolization.

  15. Three-dimensional image technology in forensic anthropology: Assessing the validity of biological profiles derived from CT-3D images of the skeleton

    Science.gov (United States)

    Garcia de Leon Valenzuela, Maria Julia

    This project explores the reliability of building a biological profile for an unknown individual based on three-dimensional (3D) images of the individual's skeleton. 3D imaging technology has been widely researched for medical and engineering applications, and it is increasingly being used as a tool for anthropological inquiry. While the question of whether a biological profile can be derived from 3D images of a skeleton with the same accuracy as achieved when using dry bones has been explored, bigger sample sizes, a standardized scanning protocol and more interobserver error data are needed before 3D methods can become widely and confidently used in forensic anthropology. 3D images of Computed Tomography (CT) scans were obtained from 130 innominate bones from Boston University's skeletal collection (School of Medicine). For each bone, both 3D images and original bones were assessed using the Phenice and Suchey-Brooks methods. Statistical analysis was used to determine the agreement between 3D image assessment versus traditional assessment. A pool of six individuals with varying experience in the field of forensic anthropology scored a subsample (n = 20) to explore interobserver error. While a high agreement was found for age and sex estimation for specimens scored by the author, the interobserver study shows that observers found it difficult to apply standard methods to 3D images. Higher levels of experience did not result in higher agreement between observers, as would be expected. Thus, a need for training in 3D visualization before applying anthropological methods to 3D bones is suggested. Future research should explore interobserver error using a larger sample size in order to test the hypothesis that training in 3D visualization will result in a higher agreement between scores. The need for the development of a standard scanning protocol focusing on the optimization of 3D image resolution is highlighted. Applications for this research include the possibility

  16. Biologically-inspired data decorrelation for hyper-spectral imaging

    Directory of Open Access Journals (Sweden)

    Ghita Ovidiu

    2011-01-01

    Full Text Available Abstract Hyper-spectral data allows the construction of more robust statistical models to sample the material properties than the standard tri-chromatic color representation. However, because of the large dimensionality and complexity of the hyper-spectral data, the extraction of robust features (image descriptors is not a trivial issue. Thus, to facilitate efficient feature extraction, decorrelation techniques are commonly applied to reduce the dimensionality of the hyper-spectral data with the aim of generating compact and highly discriminative image descriptors. Current methodologies for data decorrelation such as principal component analysis (PCA, linear discriminant analysis (LDA, wavelet decomposition (WD, or band selection methods require complex and subjective training procedures and in addition the compressed spectral information is not directly related to the physical (spectral characteristics associated with the analyzed materials. The major objective of this article is to introduce and evaluate a new data decorrelation methodology using an approach that closely emulates the human vision. The proposed data decorrelation scheme has been employed to optimally minimize the amount of redundant information contained in the highly correlated hyper-spectral bands and has been comprehensively evaluated in the context of non-ferrous material classification

  17. Prospects and challenges of quantitative phase imaging in tumor cell biology

    Science.gov (United States)

    Kemper, Björn; Götte, Martin; Greve, Burkhard; Ketelhut, Steffi

    2016-03-01

    Quantitative phase imaging (QPI) techniques provide high resolution label-free quantitative live cell imaging. Here, prospects and challenges of QPI in tumor cell biology are presented, using the example of digital holographic microscopy (DHM). It is shown that the evaluation of quantitative DHM phase images allows the retrieval of different parameter sets for quantification of cellular motion changes in migration and motility assays that are caused by genetic modifications. Furthermore, we demonstrate simultaneously label-free imaging of cell growth and morphology properties.

  18. First biological experiments at a vertical proton beam

    Energy Technology Data Exchange (ETDEWEB)

    Distel, L.; Distel, B.; Roessner, B.; Schwotzer, G.; Sauer, R. [Erlangen-Nuernberg Univ., Erlangen (Germany). Klinik fuer Strahlentherapie; Eyrich, W.; Fritsch, M.; Teufel, A. [Erlangen-Nuernberg Univ., Erlangen (Germany). Physikalisches Inst.; Besserer, J.; Boer, J. de; Moosburger, M.; Quicken, P. [Muenchen Univ. (Germany). Sektion Physik

    1997-09-01

    At the tandem accelerator laboratories in Munich and Erlangen vertical beamlines were installed last year. The advantage of a vertical beamline is that cells can be irradiated in a medium at 37 C and with simultaneous gassing, therefore also in physiological conditions. First experiments were carried out at the accelerator in Munich with a proton energy of 25 MeV. Chinese Hamster cells B14 were irradiated in Petri dishes where the base was of 1 mm polystyrol or 2 {mu}m hostaphan foils. The cell survival was measured by the cell survival assay and the repopulation of the colonies by the total colony volume. A solution of DNA with protein was irradiated to study DNA double strand breaks by constant field gel electrophoresis and DNA protein crosslinks by the nitrocellulose filter assay. For cell survival, total colony volume and DNA double-strand breaks X-rays and protons gave corresponding results, while with protons, higher yields of DNA-protein crosslinks were observed than with X-rays. (orig.)

  19. Magnetic Field Gradient Calibration as an Experiment to Illustrate Magnetic Resonance Imaging

    Science.gov (United States)

    Seedhouse, Steven J.; Hoffmann, Markus M.

    2008-01-01

    A nuclear magnetic resonance (NMR) spectroscopy experiment for the undergraduate physical chemistry laboratory is described that encompasses both qualitative and quantitative pedagogical goals. Qualitatively, the experiment illustrates how images are obtained in magnetic resonance imaging (MRI). Quantitatively, students experience the…

  20. Redefining Authentic Research Experiences in Introductory Biology Laboratories and Barriers to Their Implementation

    Science.gov (United States)

    Spell, Rachelle M.; Guinan, Judith A.; Miller, Kristen R.; Beck, Christopher W.

    2014-01-01

    Incorporating authentic research experiences in introductory biology laboratory classes would greatly expand the number of students exposed to the excitement of discovery and the rigor of the scientific process. However, the essential components of an authentic research experience and the barriers to their implementation in laboratory classes are…

  1. Cosmic-ray interaction data for designing biological experiments in space

    Science.gov (United States)

    Straume, T.; Slaba, T. C.; Bhattacharya, S.; Braby, L. A.

    2017-05-01

    There is growing interest in flying biological experiments beyond low-Earth orbit (LEO) to measure biological responses potentially relevant to those expected during a human mission to Mars. Such experiments could be payloads onboard precursor missions, including unmanned private-public partnerships, as well as small low-cost spacecraft (satellites) designed specifically for biosentinel-type missions. It is the purpose of this paper to provide physical cosmic-ray interaction data and related information useful to biologists who may be planning such experiments. It is not the objective here to actually design such experiments or provide radiobiological response functions, which would be specific for each experiment and biological endpoint. Nuclide-specific flux and dose rates were calculated using OLTARIS and these results were used to determine particle traversal rates and doses in hypothetical biological targets. Comparisons are provided between GCR in interplanetary space and inside the ISS. Calculated probabilistic estimates of dose from solar particle events are also presented. Although the focus here is on biological experiments, the information provided may be useful for designing other payloads as well if the space radiation environment is a factor to be considered.

  2. Monte Carlo modeling in CT-based geometries: dosimetry for biological modeling experiments with particle beam radiation.

    Science.gov (United States)

    Diffenderfer, Eric S; Dolney, Derek; Schaettler, Maximilian; Sanzari, Jenine K; McDonough, James; Cengel, Keith A

    2014-03-01

    The space radiation environment imposes increased dangers of exposure to ionizing radiation, particularly during a solar particle event (SPE). These events consist primarily of low energy protons that produce a highly inhomogeneous dose distribution. Due to this inherent dose heterogeneity, experiments designed to investigate the radiobiological effects of SPE radiation present difficulties in evaluating and interpreting dose to sensitive organs. To address this challenge, we used the Geant4 Monte Carlo simulation framework to develop dosimetry software that uses computed tomography (CT) images and provides radiation transport simulations incorporating all relevant physical interaction processes. We found that this simulation accurately predicts measured data in phantoms and can be applied to model dose in radiobiological experiments with animal models exposed to charged particle (electron and proton) beams. This study clearly demonstrates the value of Monte Carlo radiation transport methods for two critically interrelated uses: (i) determining the overall dose distribution and dose levels to specific organ systems for animal experiments with SPE-like radiation, and (ii) interpreting the effect of random and systematic variations in experimental variables (e.g. animal movement during long exposures) on the dose distributions and consequent biological effects from SPE-like radiation exposure. The software developed and validated in this study represents a critically important new tool that allows integration of computational and biological modeling for evaluating the biological outcomes of exposures to inhomogeneous SPE-like radiation dose distributions, and has potential applications for other environmental and therapeutic exposure simulations.

  3. Multimodal Molecular Mass Spectrometry Imaging : Development and Applications in Plant Biology and Forensic Toxicology

    OpenAIRE

    Porta, Tiffany

    2013-01-01

    This thesis focuses on the development of new analytical platforms for molecular mass spectrometry imaging and their applications in plant biology and forensic toxicology. So far, in drug metabolism or forensic toxicology, liquid chromatography with mass spectrometric detection is the technique of choice for analyzing drugs and metabolites in complex biological samples. LC-MS remains however challenging, because the development of appropriate sample preparation requires complex and time-consu...

  4. DENOTATIVE ORIGINS OF ABSTRACT IMAGES IN LINGUISTIC EXPERIMENT

    Directory of Open Access Journals (Sweden)

    Elina, E.

    2017-03-01

    Full Text Available The article discusses the refusal from denotation (the subject, as the basic principle of abstract images, and semiotic problems arising in connection with this principle: how to solve the contradiction between the pointlessness and iconic nature of the image? Is it correct in the absence of denotation to recognize abstract representation of a single-level entity? The solution is proposed to decide these questions with the help of a psycholinguistic experiment in which the verbal interpretation of abstract images made by both experienced and “naive” audience-recipients demonstrates the objectivity of perception of denotative “traces” and the presence of denotative invariant in an abstract form.

  5. Diffusion imaging with stimulated echoes: signal models and experiment design

    CERN Document Server

    Alexander, Daniel C

    2013-01-01

    Purpose: Stimulated echo acquisition mode (STEAM) diffusion MRI can be advantageous over pulsed-gradient spin-echo (PGSE) for diffusion times that are long compared to $\\ttwo$. It is important therefore for biomedical diffusion imaging applications at 7T and above where $\\ttwo$ is short. However, imaging gradients in the STEAM sequence contribute much greater diffusion weighting than in PGSE, but are often ignored during post-processing. We demonstrate here that this can severely bias parameter estimates. Method: We present models for the STEAM signal for free and restricted diffusion that account for crusher and slice-select (butterfly) gradients to avoid such bias. The butterfly gradients also disrupt experiment design, typically by skewing gradient-vectors towards the slice direction. We propose a simple compensation to the diffusion gradient vector specified to the scanner that counterbalances the butterfly gradients to preserve the intended experiment design. Results: High-field data fixed monkey brain e...

  6. Texture analysis methods for the characterisation of biological and medical images

    Directory of Open Access Journals (Sweden)

    Ştefan Ţălu

    2012-06-01

    Full Text Available Adaptations can be extreme in many cases and they help organisms survive in their habitat or ecological niche. These adaptations can affect their anatomy, ethology or physiology. Anatomical adaptations are physical features such as animal's shape, particularities at the skeleton level, texture of exoskeleton, surface of the skin in animals or cuticula in plants etc. The purpose of this paper is to present a synthesis concerning the texture analysis methods used for the characterisation of biological and medical images. Texture analysis methods of biological and medical images provide noninvasive tools that allow biologists, physicians and researchers the early detection and diagnosis of diseases.

  7. A sidelobe suppression method with experiment for underwater acoustic imaging

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In this paper,a sidelobe suppression method using nonuniformly spaced array with aperture apodization processing is proposed for underwater acoustic imaging in near field,which is studied both in theory and experiment.The focused beamforming based on spherical wave propagation theory is used in the method.Firstly,the nonuniform array with low sidelobe is designed for suppressing the sidelobe of one-way beam pattern by spacing perturbation.Then, applying the aperture apodization technique to underwater ac...

  8. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language

    National Research Council Canada - National Science Library

    Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

    2011-01-01

    .... In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments...

  9. BIOSPEX: Biological space experiments, a compendium of life sciences experiments carried on US spacecraft

    Science.gov (United States)

    Anderson, M.; Rummel, J. A. (Editor); Deutsch, S. (Editor)

    1979-01-01

    United States space life science experiments, encompassing 27 years of experience beginning with sounding rocket flights carrying primates (1948) to the last U.S. spaceflight, the joint US/USSR Apollo Test Project (1975), are presented. The information for each experiment includes Principal Investigators, the program and mission on which it was flown, the specimens used, the objectives, protocol, equipment, results, conclusions, and bibliographic reference citations for publications derived from each experiment.

  10. Coherent anti-stokes Raman scattering microscopy: chemical imaging for biology and medicine.

    Science.gov (United States)

    Evans, Conor L; Xie, X Sunney

    2008-01-01

    Coherent anti-Stokes Raman scattering (CARS) microscopy is a label-free imaging technique that is capable of real-time, nonperturbative examination of living cells and organisms based on molecular vibrational spectroscopy. Recent advances in detection schemes, understanding of contrast mechanisms, and developments of laser sources have enabled superb sensitivity and high time resolution. Emerging applications, such as metabolite and drug imaging and tumor identification, raise many exciting new possibilities for biology and medicine.

  11. Identifying Multiple Potential Metabolic Cycles in Time-Series from Biolog Experiments

    OpenAIRE

    Shubin, Mikhail; Schaufler, Katharina; Tedin, Karsten; Vehkala, Minna; Corander, Jukka

    2016-01-01

    Biolog Phenotype Microarray (PM) is a technology allowing simultaneous screening of the metabolic behaviour of bacteria under a large number of different conditions. Bacteria may often undergo several cycles of metabolic activity during a Biolog experiment. We introduce a novel algorithm to identify these metabolic cycles in PM experimental data, thus increasing the potential of PM technology in microbiology. Our method is based on a statistical decomposition of the time-series measurements i...

  12. Biological imaging without autofluorescence in the second near-infrared region

    Institute of Scientific and Technical Information of China (English)

    Shuo Diao[1; Guosong Hong[1; Alexander L. Antaris[1; Jeffrey L. Blackbum[2; Kai Cheng[3; Zhen Cheng[3; Hongjie Dai[1

    2015-01-01

    Fluorescence imaging is capable of acquiring anatomical and functional infor- mation with high spatial and temporal resolution. This imaging technique has been indispensable in biological research and disease detection/diagnosis. Imaging in the visible and to a lesser degree, in the near-infrared (NIR) regions below 900 nm, suffers from autofluorescence arising from endogenous fluorescent molecules in biological tissues. This autofluorescence interferes with fluorescent molecules of interest, causing a high background and low detection sensitivity. Here, we report that fluorescence imaging in the 1,500-1,700-nm region (termed "NIR-IIb") under 808-nm excitation results in nearly zero tissue autofluorescence, allowing for background-free imaging of fluorescent species in otherwise notoriously autofluorescent biological tissues, including liver. Imaging of the intrinsic fluorescence of individual fluorophores, such as a single carbon nanotube, can be readily achieved with high sensitivity and without autofluorescence background in mouse liver within the 1,500-1,700-nm wavelength region.

  13. Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images

    Directory of Open Access Journals (Sweden)

    Kimori Yoshitaka

    2010-07-01

    Full Text Available Abstract Background A reliable extraction technique for resolving multiple spots in light or electron microscopic images is essential in investigations of the spatial distribution and dynamics of specific proteins inside cells and tissues. Currently, automatic spot extraction and characterization in complex microscopic images poses many challenges to conventional image processing methods. Results A new method to extract closely located, small target spots from biological images is proposed. This method starts with a simple but practical operation based on the extended morphological top-hat transformation to subtract an uneven background. The core of our novel approach is the following: first, the original image is rotated in an arbitrary direction and each rotated image is opened with a single straight line-segment structuring element. Second, the opened images are unified and then subtracted from the original image. To evaluate these procedures, model images of simulated spots with closely located targets were created and the efficacy of our method was compared to that of conventional morphological filtering methods. The results showed the better performance of our method. The spots of real microscope images can be quantified to confirm that the method is applicable in a given practice. Conclusions Our method achieved effective spot extraction under various image conditions, including aggregated target spots, poor signal-to-noise ratio, and large variations in the background intensity. Furthermore, it has no restrictions with respect to the shape of the extracted spots. The features of our method allow its broad application in biological and biomedical image information analysis.

  14. Imaging of Selenium by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in 2-D Electrophoresis Gels and Biological Tissues.

    Science.gov (United States)

    Cruz, Elisa Castañeda Santa; Susanne Becker, J; Sabine Becker, J; Sussulini, Alessandra

    2018-01-01

    Selenium and selenoproteins are important components of living organisms that play a role in different biological processes. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful analytical technique that has been employed to obtain distribution maps of selenium in biological tissues in a direct manner, as well as in selenoproteins, previously separated by their molecular masses and isoelectric points using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In this chapter, we present the protocols to perform LA-ICP-MS imaging experiments, allowing the distribution visualization and determination of selenium and/or selenoproteins in biological systems.

  15. The Ring Imaging CHerenkov Detectors of the LHCb Experiment

    CERN Document Server

    Perego, Davide Luigi

    2012-01-01

    Particle identification is a fundamental requirement of the LHCb experiment to fulfill its physics programme. Positive hadron identification is performed by two Ring Imaging CHerenkov (RICH) detectors. This system covers the full angular acceptance of the experiment and is equipped with three Cherenkov radiators to identify particles in a wide momentum range from1 GeV/ c up to 100 GeV/ c . The Hybrid Photon Detectors (HPDs) located outside the detector acceptance provide the photon detection with 500,000 channels. Specific read–out electronics has been developed to readout and process data from the HPDs including data transmission and power distribution. The operation and performanceoftheRICHsystemare ensuredbythe constant controland monitoringoflowandhighvoltage systems,of thegas qualityandenvironmental parameters,ofthe mirror alignment,and finallyofthe detector safety. The description of the LHCb RICH is given. The experience in operating the detector at the Large Hadron Collider is presented and discusse...

  16. Students' Ideas about Prismatic Images: Teaching Experiments for an Image-Based Approach

    Science.gov (United States)

    Grusche, Sascha

    2017-01-01

    Prismatic refraction is a classic topic in science education. To investigate how undergraduate students think about prismatic dispersion, and to see how they change their thinking when observing dispersed images, five teaching experiments were done and analysed according to the Model of Educational Reconstruction. For projection through a prism,…

  17. Mass spectrometry imaging of biological tissue : an approach for multicenter studies

    NARCIS (Netherlands)

    Römpp, Andreas; Both, Jean-Pierre; Brunelle, Alain; Heeren, Ron M A; Laprévote, Olivier; Prideaux, Brendan; Seyer, Alexandre; Spengler, Bernhard; Stoeckli, Markus; Smith, Donald F

    2015-01-01

    Mass spectrometry imaging has become a popular tool for probing the chemical complexity of biological surfaces. This led to the development of a wide range of instrumentation and preparation protocols. It is thus desirable to evaluate and compare the data output from different methodologies and mass

  18. Image of Synthetic Biology and Nanotechnology: A Survey among University Students

    Directory of Open Access Journals (Sweden)

    Christian Ineichen

    2017-09-01

    Full Text Available This study explores the image of synthetic biology and nanotechnology in comparison to agricultural biotechnology and communication technology by examining spontaneous associations with, and deliberate evaluations of, these technologies by university students. Data were collected through a self-completion online questionnaire by students from two universities in Switzerland. The survey aimed to capture implicit associations, explicit harm-benefit evaluations and views on regulation. The data suggest overall positive associations with emerging technologies. While positive associations were most pronounced for nanotechnology, agricultural biotechnology was attributed with the least favorable associations. In contrast to its positive result in the association task, respondents attributed a high harm potential for nanotechnology. Associations attributed to synthetic biology were demonstrated to be more positive than for agricultural biotechnology, however, not as favorable as for nanotechnology. Contrary to the evaluations of nanotechnology, the benefit-examples of synthetic biology were evaluated particularly positively. Accordingly, the investigated technologies enjoy different esteem, with synthetic biology and nanotechnology both showing a more “exciting” image. Even though, the image of nanotechnology was demonstrated to be more pronounced it was also more heterogeneous across tasks while agricultural biotechnology remains contested. For all technologies, the predominant spontaneous concerns pertain to risks rather than an immoral nature inherent to these technologies. Our data suggest that harm-benefit analyses reveal only one aspect of the attitude toward emerging technologies. Survey questions addressing spontaneous associations with these technologies are a valuable addition for our picture of the image of emerging technologies.

  19. Application of gold thin-films for internal standardization in LA-ICP-MS imaging experiments.

    Science.gov (United States)

    Bonta, Maximilian; Lohninger, Hans; Marchetti-Deschmann, Martina; Limbeck, Andreas

    2014-03-21

    LA-ICP-MS imaging experiments are of growing interest within the field of biosciences. Revealing the distributions of major components as well as trace elements in biological samples can help to understand fundamental biological processes. However, highly variable sample conditions and changing instrumental parameters during measurement time aggravate reliable quantification especially in biological tissues. Normally matrix matched standards used for calibration are scarcely available and the manufacturing process thereof is rather complicated. Thus most experiments reported in the literature only delivered qualitative information on the analyte distributions. The use of appropriate internal standards facilitates the preparation of calibrations even without the utilization of matrix-matched standards. In the presented work an approach for providing reliable quantitative bio-images is proposed using gold thin-layers as an internal standard and patterns printed with commercially available inkjet printers as standards. The method development is based on copper from blue ink as the element of interest. It could be shown that gold standardization compensates instrumental drifts, matrix related ablation differences and day-to-day signal changes. Not only was the quality of the obtained images improved by gold standardization; while the relative standard deviation of the measurements was around 15% before standardization it could be decreased to less than 5% by gold standardization. Also quantitative information could be obtained for samples with unknown analyte concentrations. Depending on the used beam diameter limits of detection in the range of some hundreds ng g(-1) were achieved. The presented method is a promising and easy-to-handle alternative to matrix matched standards for signal quantification.

  20. Elemental and isotopic imaging of biological samples using NanoSIMS.

    Science.gov (United States)

    Kilburn, Matt R; Clode, Peta L

    2014-01-01

    With its low detection limits and the ability to analyze most of the elements in the periodic table, secondary ion mass spectrometry (SIMS) represents one of the most versatile in situ analytical techniques available, and recent developments have resulted in significant advantages for the use of imaging mass spectrometry in biological and biomedical research. Increases in spatial resolution and sensitivity allow detailed interrogation of samples at relevant scales and chemical concentrations. Advances in dynamic SIMS, specifically with the advent of NanoSIMS, now allow the tracking of stable isotopes within biological systems at subcellular length scales, while static SIMS combines subcellular imaging with molecular identification. In this chapter, we present an introduction to the SIMS technique, with particular reference to NanoSIMS, and discuss its application in biological and biomedical research.

  1. Usefulness of biological fingerprint in magnetic resonance imaging for patient verification.

    Science.gov (United States)

    Ueda, Yasuyuki; Morishita, Junji; Kudomi, Shohei; Ueda, Katsuhiko

    2016-09-01

    The purpose of our study is to investigate the feasibility of automated patient verification using multi-planar reconstruction (MPR) images generated from three-dimensional magnetic resonance (MR) imaging of the brain. Several anatomy-related MPR images generated from three-dimensional fast scout scan of each MR examination were used as biological fingerprint images in this study. The database of this study consisted of 730 temporal pairs of MR examination of the brain. We calculated the correlation value between current and prior biological fingerprint images of the same patient and also all combinations of two images for different patients to evaluate the effectiveness of our method for patient verification. The best performance of our system were as follows: a half-total error rate of 1.59 % with a false acceptance rate of 0.023 % and a false rejection rate of 3.15 %, an equal error rate of 1.37 %, and a rank-one identification rate of 98.6 %. Our method makes it possible to verify the identity of the patient using only some existing medical images without the addition of incidental equipment. Also, our method will contribute to patient misidentification error management caused by human errors.

  2. Identification of new pancreatic beta cell targets for in vivo imaging by a systems biology approach.

    Science.gov (United States)

    Bouckenooghe, Thomas; Flamez, Daisy; Ortis, Fernanda; Goldman, Serge; Eizirik, Decio L

    2010-05-01

    Systems biology is an emergent field that aims to understand biological systems at system-level. The increasing power of genome sequencing techniques and ranges of other molecular biology techniques is enabling the accumulation of in-depth knowledge of biological systems. This growing information, properly quantified, analysed and presented, will eventually allow the establishment of a system-based cartography of different cellular populations within the organism, and of their interactions at the tissue and organ levels. It will also allow the identification of specific markers of individual cell types. Systems biology approaches to discover diagnostic markers may have an important role in diabetes. There are presently no reliable ways to quantify beta cell mass (BCM) in vivo, which hampers the understanding of the pathogenesis and natural history of diabetes, and the development of novel therapies to preserve BCM. To solve this problem, novel and specific beta cell biomarkers must be identified to enable adequate in vivo imaging by methods such as Positron Emission Tomography (PET). The ideal biomarker should allow measurements by a minimally invasive technology enabling repeated examinations over time, should identify the early stages of decreased BCM, and should provide information on progression of beta cell loss and eventual responses to agents aiming to arrest or revert beta cell loss in diabetes. The present review briefly describes the "state-of-the-art" in the field, and then proposes a step-by-step systems biology approach for the identification and initial testing of novel candidates for beta cell imaging.

  3. An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments.

    Science.gov (United States)

    Oetjen, Janina; Lachmund, Delf; Palmer, Andrew; Alexandrov, Theodore; Becker, Michael; Boskamp, Tobias; Maass, Peter

    2016-09-01

    A standardized workflow for matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI imaging MS) is a prerequisite for the routine use of this promising technology in clinical applications. We present an approach to develop standard operating procedures for MALDI imaging MS sample preparation of formalin-fixed and paraffin-embedded (FFPE) tissue sections based on a novel quantitative measure of dataset quality. To cover many parts of the complex workflow and simultaneously test several parameters, experiments were planned according to a fractional factorial design of experiments (DoE). The effect of ten different experiment parameters was investigated in two distinct DoE sets, each consisting of eight experiments. FFPE rat brain sections were used as standard material because of low biological variance. The mean peak intensity and a recently proposed spatial complexity measure were calculated for a list of 26 predefined peptides obtained by in silico digestion of five different proteins and served as quality criteria. A five-way analysis of variance (ANOVA) was applied on the final scores to retrieve a ranking of experiment parameters with increasing impact on data variance. Graphical abstract MALDI imaging experiments were planned according to fractional factorial design of experiments for the parameters under study. Selected peptide images were evaluated by the chosen quality metric (structure and intensity for a given peak list), and the calculated values were used as an input for the ANOVA. The parameters with the highest impact on the quality were deduced and SOPs recommended.

  4. Microwave thermal imaging of scanned focused ultrasound heating: animal experiments

    Science.gov (United States)

    Zhou, Tian; Meaney, Paul M.; Hoopes, P. Jack; Geimer, Shireen D.; Paulsen, Keith D.

    2011-03-01

    High intensity focused ultrasound (HIFU) uses focused ultrasound beams to ablate localized tumors noninvasively. Multiple clinical trials using HIFU treatment of liver, kidney, breast, pancreas and brain tumors have been conducted, while monitoring the temperature distribution with various imaging modalities such as MRI, CT and ultrasound. HIFU has achieved only minimal acceptance partially due to insufficient guidance from the limited temperature monitoring capability and availability. MR proton resonance frequency (PRF) shift thermometry is currently the most effective monitoring method; however, it is insensitive in temperature changes in fat, susceptible to motion artifacts, and is high cost. Exploiting the relationship between dielectric properties (i.e. permittivity and conductivity) and tissue temperature, in vivo dielectric property distributions of tissue during heating were reconstructed with our microwave tomographic imaging technology. Previous phantom studies have demonstrated sub-Celsius temperature accuracy and sub-centimeter spatial resolution in microwave thermal imaging. In this paper, initial animal experiments have been conducted to further investigate its potential. In vivo conductivity changes inside the piglet's liver due to focused ultrasound heating were observed in the microwave images with good correlation between conductivity changes and temperature.

  5. Noninvasive imaging analysis of biological tissue associated with laser thermal injury.

    Science.gov (United States)

    Chang, Cheng-Jen; Yu, De-Yi; Hsiao, Yen-Chang; Ho, Kuang-Hua

    2017-04-01

    The purpose of our study is to use a noninvasive tomographic imaging technique with high spatial resolution to characterize and monitor biological tissue responses associated with laser thermal injury. Optical doppler tomography (ODT) combines laser doppler flowmetry (LDF) with optical coherence tomography (OCT) to obtain high resolution tomographic velocity and structural images of static and moving constituents in highly scattering biological tissues. A SurgiLase XJ150 carbon dioxide (CO2) laser using a continuous mode of 3 watts (W) was used to create first, second or third degree burns on anesthetized Sprague-Dawley rats. Additional parameters for laser thermal injury were assessed as well. The rationale for using ODT in the evaluation of laser thermal injury offers a means of constructing a high resolution tomographic image of the structure and perfusion of laser damaged skin. In the velocity images, the blood flow is coded at 1300 μm/s and 0 velocity, 1000 μm/s and 0 velocity, 700 μm/s and 0 velocity adjacent to the first, second, and third degree injuries, respectively. ODT produces exceptional spatial resolution while having a non-invasive way of measurement, therefore, ODT is an accurate measuring method for high-resolution fluid flow velocity and structural images for biological tissue with laser thermal injury. Copyright © 2017 Chang Gung University. Published by Elsevier B.V. All rights reserved.

  6. The image of cell in biology books: an approach from Cognitive Theory of Multimedia Learning

    Directory of Open Access Journals (Sweden)

    Ricardo Ferreira das Neves

    2016-04-01

    Full Text Available The research aimed to analyze the didactic value (VD of the images related to the concept of cell in biology books of High School and Higher Education, supported by Cognitivist Theory of Multimedia Learning (TCAM. With the technological advent there was a better development of the layout of production techniques and layout of the images in books, in order to help the study of abstract concepts and often complex, such as the cell. However sometimes it not happens. From the application of TCAM principles, we noted that the images related to cell concept presented VD elements with deviations on the principles of Consistency, Signaling and Spatial Contiguity, with great emphasis to the last one. It is necessary to establish eligibility criteria and inclusion of images in books, because the images represent potential resource to reduce abstraction and to facilitate conceptual learning.

  7. The MARTE VNIR Imaging Spectrometer Experiment: Design and Analysis

    CERN Document Server

    Brown, Adrian J; Dunagan, Stephen

    2014-01-01

    We report on the design, operation, and data analysis methods employed on the VNIR imaging spectrometer instrument that was part of the Mars Astrobiology Research and Technology Experiment (MARTE). The imaging spectrometer is a hyperspectral scanning pushbroom device sensitive to VNIR wavelengths from 400-1000 nm. During the MARTE project, the spectrometer was deployed to the Rio Tinto region of Spain. We analyzed subsets of 3 cores from Rio Tinto using a new band modeling technique. We found most of the MARTE drill cores to contain predominantly goethite, though spatially coherent areas of hematite were identified in Core 23. We also distinguished non Fe-bearing minerals that were subsequently analyzed by X-ray diffraction (XRD) and found to be primarily muscovite. We present drill core maps that include spectra of goethite, hematite, and non Fe-bearing minerals.

  8. Biological Database of Images and Genomes: tools for community annotations linking image and genomic information

    Science.gov (United States)

    Oberlin, Andrew T; Jurkovic, Dominika A; Balish, Mitchell F; Friedberg, Iddo

    2013-01-01

    Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype–genotype connection linking the two types of data is lagging behind. While there are many types of software that enable the manipulation and analysis of image data and genomic data as separate entities, there is no framework established for linking the two. We present a generic set of software tools, BioDIG, that allows linking of image data to genomic data. BioDIG tools can be applied to a wide range of research problems that require linking images to genomes. BioDIG features the following: rapid construction of web-based workbenches, community-based annotation, user management and web services. By using BioDIG to create websites, researchers and curators can rapidly annotate a large number of images with genomic information. Here we present the BioDIG software tools that include an image module, a genome module and a user management module. We also introduce a BioDIG-based website, MyDIG, which is being used to annotate images of mycoplasmas. Database URL: BioDIG website: http://biodig.org BioDIG source code repository: http://github.com/FriedbergLab/BioDIG The MyDIG database: http://mydig.biodig.org/ PMID:23550062

  9. Image processing analysis of traditional Gestalt vision experiments

    Science.gov (United States)

    McCann, John J.

    2002-06-01

    In the late 19th century, the Gestalt Psychology rebelled against the popular new science of Psychophysics. The Gestalt revolution used many fascinating visual examples to illustrate that the whole is greater than the sum of all the parts. Color constancy was an important example. The physical interpretation of sensations and their quantification by JNDs and Weber fractions were met with innumerable examples in which two 'identical' physical stimuli did not look the same. The fact that large changes in the color of the illumination failed to change color appearance in real scenes demanded something more than quantifying the psychophysical response of a single pixel. The debates continues today with proponents of both physical, pixel-based colorimetry and perceptual, image- based cognitive interpretations. Modern instrumentation has made colorimetric pixel measurement universal. As well, new examples of unconscious inference continue to be reported in the literature. Image processing provides a new way of analyzing familiar Gestalt displays. Since the pioneering experiments by Fergus Campbell and Land, we know that human vision has independent spatial channels and independent color channels. Color matching data from color constancy experiments agrees with spatial comparison analysis. In this analysis, simple spatial processes can explain the different appearances of 'identical' stimuli by analyzing the multiresolution spatial properties of their surrounds. Benary's Cross, White's Effect, the Checkerboard Illusion and the Dungeon Illusion can all be understood by the analysis of their low-spatial-frequency components. Just as with color constancy, these Gestalt images are most simply described by the analysis of spatial components. Simple spatial mechanisms account for the appearance of 'identical' stimuli in complex scenes. It does not require complex, cognitive processes to calculate appearances in familiar Gestalt experiments.

  10. Two Different Bifurcation Scenarios in Neural Firing Rhythms Discovered in Biological Experiments by Adjusting Two Parameters

    Institute of Scientific and Technical Information of China (English)

    WV Xiao-Bo; MO Juan; YANG Ming-Hao; ZHENG Qiao-Hua; GU Hua-Guang; HEN Wei

    2008-01-01

    @@ Two different bifurcation scenarios, one is novel and the other is relatively simpler, in the transition procedures of neural firing patterns are studied in biological experiments on a neural pacemaker by adjusting two parameters. The experimental observations are simulated with a relevant theoretical model neuron. The deterministic non-periodic firing pattern lying within the novel bifurcation scenario is suggested to be a new case of chaos, which has not been observed in previous neurodynamical experiments.

  11. Identifying Multiple Potential Metabolic Cycles in Time-Series from Biolog Experiments.

    Science.gov (United States)

    Shubin, Mikhail; Schaufler, Katharina; Tedin, Karsten; Vehkala, Minna; Corander, Jukka

    Biolog Phenotype Microarray (PM) is a technology allowing simultaneous screening of the metabolic behaviour of bacteria under a large number of different conditions. Bacteria may often undergo several cycles of metabolic activity during a Biolog experiment. We introduce a novel algorithm to identify these metabolic cycles in PM experimental data, thus increasing the potential of PM technology in microbiology. Our method is based on a statistical decomposition of the time-series measurements into a set of growth models. We show that the method is robust to measurement noise and captures accurately the biologically relevant signals from the data. Our implementation is made freely available as a part of an R package for PM data analysis and can be found at www.helsinki.fi/bsg/software/Biolog_Decomposition.

  12. Experiments on terahertz 3D scanning microscopic imaging

    Science.gov (United States)

    Zhou, Yi; Li, Qi

    2016-10-01

    Compared with the visible light and infrared, terahertz (THz) radiation can penetrate nonpolar and nonmetallic materials. There are many studies on the THz coaxial transmission confocal microscopy currently. But few researches on the THz dual-axis reflective confocal microscopy were reported. In this paper, we utilized a dual-axis reflective confocal scanning microscope working at 2.52 THz. In contrast with the THz coaxial transmission confocal microscope, the microscope adopted in this paper can attain higher axial resolution at the expense of reduced lateral resolution, revealing more satisfying 3D imaging capability. Objects such as Chinese characters "Zhong-Hua" written in paper with a pencil and a combined sheet metal which has three layers were scanned. The experimental results indicate that the system can extract two Chinese characters "Zhong," "Hua" or three layers of the combined sheet metal. It can be predicted that the microscope can be applied to biology, medicine and other fields in the future due to its favorable 3D imaging capability.

  13. Variability of Biological Degradation of Aromatic Hydrocarbons in an Aerobic Aquifer Determined by Laboratory Batch Experiments

    DEFF Research Database (Denmark)

    Nielsen, Per Henning; Christensen, Thomas Højlund

    1994-01-01

    The biological aerobic degradation of 7 aromatic hydrocarbons (benzene, toluene, o-xylene, p-dichlorobenzene, o-dichlorobenzene, naphthalene and biphenyl) was studied for 149 days in replicate laboratory batch experiments with groundwater and sediment from 8 localities representing a 15 m × 30 m...... section of an aerobic aquifer. Compared to biologically deactivated control experiments all compounds were biologically degraded. Degradation curves were very reproducible for some compounds (benzene, toluene, o-xylene, o-dichlorobenzene and p-dichlorobenzene) and less reproducible for other (naphthalene......, naphthlene and biphenyl, but not for o-xylene, o-dichlorobenzene, and p-dichlorobenzene. The maximum variation in degradation rates was 15 times in the case of biphenyl. Significant co-variation in degradation rates was found between benzene and toluene, and between p- and o-dichlorobenzene....

  14. Proceedings of the 2006 International Workshop on Multiscale Biological Imaging, Data Mining and Informatics, Santa Barbara, USA (BII06).

    Science.gov (United States)

    2007-07-10

    The 2006 International Workshop on Multiscale Biological Imaging, Data Mining and Informatics was held at Santa Barbara, on Sept 7-8, 2006. Based on the presentations at the workshop, we selected and compiled this collection of research articles related to novel algorithms and enabling techniques for bio- and biomedical image analysis, mining, visualization, and biology applications.

  15. Field Biology Experiences of Undergraduate Students: The Impact of Novelty Space

    Science.gov (United States)

    Cotton, Debby R. E.; Cotton, Peter A.

    2009-01-01

    Fieldwork is generally considered an essential aspect of teaching and learning about biology, at both school and university level. However, previous research suggests that the novelty of being in an unfamiliar field environment can negatively, as well as positively, impact on the student experience and learning. This research uses the framework of…

  16. Variability of Biological Degradation of Aromatic Hydrocarbons in an Aerobic Aquifer Determined by Laboratory Batch Experiments

    DEFF Research Database (Denmark)

    Nielsen, Per Henning; Christensen, Thomas Højlund

    1994-01-01

    The biological aerobic degradation of 7 aromatic hydrocarbons (benzene, toluene, o-xylene, p-dichlorobenzene, o-dichlorobenzene, naphthalene and biphenyl) was studied for 149 days in replicate laboratory batch experiments with groundwater and sediment from 8 localities representing a 15 m × 30 m...

  17. Introduction to Biological Investigations: A First-Year Experience in Experimental Design and Scientific Communication

    Science.gov (United States)

    Foote, Linda C.; Fitzpatrick, Kathleen A.

    2004-01-01

    Introduction to Biological Investigations is a course that was developed to introduce the scientific method through practical application. This active, student-centered experience fosters fundamental skills that promote creativity, critical thinking, and scientific-communication. The course has been well received by first-year students, and…

  18. Simulation and Experiment of Extinction or Adaptation of Biological Species after Temperature Changes

    Science.gov (United States)

    Stauffer, D.; Arndt, H.

    Can unicellular organisms survive a drastic temperature change, and adapt to it after many generations? In simulations of the Penna model of biological aging, both extinction and adaptation were found for asexual and sexual reproduction as well as for parasex. These model investigations are the basis for the design of evolution experiments with heterotrophic flagellates.

  19. High Mass Accuracy and High Mass Resolving Power FT-ICR Secondary Ion Mass Spectrometry for Biological Tissue Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Donald F.; Kiss, Andras; Leach, Franklin E.; Robinson, Errol W.; Pasa-Tolic, Ljiljana; Heeren, Ronald M.

    2013-07-01

    Biological tissue imaging by secondary ion mass spectrometry has seen rapid development with the commercial availability of polyatomic primary ion sources. Endogenous lipids and other small bio-molecules can now be routinely mapped on the micrometer scale. Such experiments are typically performed on time-of-flight mass spectrometers for high sensitivity and high repetition rate imaging. However, such mass analyzers lack the mass resolving power to ensure separation of isobaric ions and the mass accuracy for exact mass elemental formula assignment. We have recently reported a secondary ion mass spectrometer with the combination of a C60 primary ion gun with a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for high mass resolving power, high mass measurement accuracy and tandem mass spectrometry capabilities. In this work, high specificity and high sensitivity secondary ion FT-ICR MS was applied to chemical imaging of biological tissue. An entire rat brain tissue was measured with 150 μm spatial resolution (75 μm primary ion spot size) with mass resolving power (m/Δm50%) of 67,500 (at m/z 750) and root-mean-square measurement accuracy less than two parts-per-million for intact phospholipids, small molecules and fragments. For the first time, ultra-high mass resolving power SIMS has been demonstrated, with m/Δm50% > 3,000,000. Higher spatial resolution capabilities of the platform were tested at a spatial resolution of 20 μm. The results represent order of magnitude improvements in mass resolving power and mass measurement accuracy for SIMS imaging and the promise of the platform for ultra-high mass resolving power and high spatial resolution imaging.

  20. Solid Hydrogen Experiments for Atomic Propellants: Image Analyses

    Science.gov (United States)

    Palaszewski, Bryan

    2002-01-01

    This paper presents the results of detailed analyses of the images from experiments that were conducted on the formation of solid hydrogen particles in liquid helium. Solid particles of hydrogen were frozen in liquid helium, and observed with a video camera. The solid hydrogen particle sizes, their agglomerates, and the total mass of hydrogen particles were estimated. Particle sizes of 1.9 to 8 mm (0.075 to 0.315 in.) were measured. The particle agglomerate sizes and areas were measured, and the total mass of solid hydrogen was computed. A total mass of from 0.22 to 7.9 grams of hydrogen was frozen. Compaction and expansion of the agglomerate implied that the particles remain independent particles, and can be separated and controlled. These experiment image analyses are one of the first steps toward visually characterizing these particles, and allow designers to understand what issues must be addressed in atomic propellant feed system designs for future aerospace vehicles.

  1. Novel photoluminescence-enhancing substrates for image formation of biological objects

    CERN Document Server

    Dovbeshko, G I; Boyko, V V; Gorchev, V F; Karakhin, S O; Gridina, N Ya; Gorelik, V S; Moiseenko, V N

    2012-01-01

    The use of photonic crystals, which were fabricated on the basis of synthetic opals, as substrates for the luminescence microscopy of biological objects has been shown. The spatial distributions of the photoluminescence by DNA clusters excited by 365-nm ultraviolet irradiation on opal surfaces and rough gold substrates have been studied. With the use of blood cells as an example, a possibility for the visualization of biological objects in the case where the nanostructure elements of synthetic opals are applied as labels and image amplifiers has been demonstrated.

  2. In Vivo Bioluminescent Imaging (BLI: Noninvasive Visualization and Interrogation of Biological Processes in Living Animals

    Directory of Open Access Journals (Sweden)

    Steven Ripp

    2010-12-01

    Full Text Available In vivo bioluminescent imaging (BLI is increasingly being utilized as a method for modern biological research. This process, which involves the noninvasive interrogation of living animals using light emitted from luciferase-expressing bioreporter cells, has been applied to study a wide range of biomolecular functions such as gene function, drug discovery and development, cellular trafficking, protein-protein interactions, and especially tumorigenesis, cancer treatment, and disease progression. This article will review the various bioreporter/biosensor integrations of BLI and discuss how BLI is being applied towards a new visual understanding of biological processes within the living organism.

  3. In Vivo Bioluminescent Imaging (BLI): Noninvasive Visualization and Interrogation of Biological Processes in Living Animals

    Science.gov (United States)

    Close, Dan M.; Xu, Tingting; Sayler, Gary S.; Ripp, Steven

    2011-01-01

    In vivo bioluminescent imaging (BLI) is increasingly being utilized as a method for modern biological research. This process, which involves the noninvasive interrogation of living animals using light emitted from luciferase-expressing bioreporter cells, has been applied to study a wide range of biomolecular functions such as gene function, drug discovery and development, cellular trafficking, protein-protein interactions, and especially tumorigenesis, cancer treatment, and disease progression. This article will review the various bioreporter/biosensor integrations of BLI and discuss how BLI is being applied towards a new visual understanding of biological processes within the living organism. PMID:22346573

  4. Imaging mass spectrometry: enabling a new age of discovery in biology and medicine through molecular microscopy.

    Science.gov (United States)

    Caprioli, Richard M

    2015-06-01

    Imaging mass spectrometry (IMS) has become a valuable tool for the production of molecular maps in samples ranging from solid inorganic materials to biologicals such as cells and tissues. The unique features of IMS are its ability to map a wide variety of different types of molecules, its superb molecular specificity, and its potential for discovery since no target-specific reagents are needed. IMS has made significant contributions in biology and medicine and promises to be a next generation tool in anatomic pathology.

  5. Historical parallels of biological space experiments from Soyuz, Salyut and Mir to Shenzhou flights

    Science.gov (United States)

    Nechitailo, Galina S.; Kondyurin, Alexey

    2016-07-01

    Human exploitation of space is a great achievement of our civilization. After the first space flights a development of artificial biological environment in space systems is a second big step. First successful biological experiments on a board of space station were performed on Salyut and Mir stations in 70-90th of last century such as - first long time cultivation of plants in space (wheat, linen, lettuce, crepis); - first flowers in space (Arabidopsis); - first harvesting of seeds in space (Arabidopsis); - first harvesting of roots (radish); - first full life cycle from seeds to seeds in space (wheat), Guinness recorded; - first tissue culture experiments (Panax ginseng L, Crocus sativus L, Stevia rebaundiana B; - first tree growing in space for 2 years (Limonia acidissima), Guinness recorded. As a new wave, the modern experiments on a board of Shenzhou Chinese space ships are performed with plants and tissue culture. The space flight experiments are now focused on applications of the space biology results to Earth technologies. In particular, the tomato seeds exposed 6 years in space are used in pharmacy industry in more then 10 pharmaceutical products. Tissue culture experiments are performed on the board of Shenzhou spaceship for creation of new bioproducts including Space Panax ginseng, Space Spirulina, Space Stetatin, Space Tomato and others products with unique properties. Space investments come back.

  6. Numerical analysis of biological clogging in two-dimensional sand box experiments

    DEFF Research Database (Denmark)

    Kildsgaard, J.; Engesgaard, Peter Knudegaard

    2001-01-01

    Two-dimensional models for biological clogging and sorptive tracer transport were used to study the progress of clogging in a sand box experiment. The sand box had been inoculated with a strip of bacteria and exposed to a continuous injection of nitrate and acetate. Brilliant Blue was regularly...... with the assumed linear constant Kd behaviour. It is demonstrated that the dimensionality of sand box experiments in comparison to column experiments results in a much lower reduction in hydraulic conductivity Žfactor of 100. and that the bulk hydraulic conductivity of the sand box decreased only slightly. However...

  7. Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology.

    Directory of Open Access Journals (Sweden)

    David A Ball

    Full Text Available The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists frequently perform gene expression studies that require changes in growth conditions to characterize the stability of switches, the transfer function of a genetic device, or the oscillations of gene networks. It is rarely possible to know a priori at what times the various changes should be made, and the success of the experiment is unknown until all of the image processing is completed well after the completion of the experiment. This results in wasted time and resources, due to the need to repeat the experiment to fine-tune the imaging parameters. To overcome this limitation, we have developed an adaptive imaging platform called GenoSIGHT that processes images as they are recorded, and uses the resulting data to make real-time adjustments to experimental conditions. We have validated this closed-loop control of the experiment using galactose-inducible expression of the yellow fluorescent protein Venus in Saccharomyces cerevisiae. We show that adaptive imaging improves the reproducibility of gene expression data resulting in more accurate estimates of gene network parameters while increasing productivity ten-fold.

  8. Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology.

    Science.gov (United States)

    Ball, David A; Lux, Matthew W; Adames, Neil R; Peccoud, Jean

    2014-01-01

    The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists frequently perform gene expression studies that require changes in growth conditions to characterize the stability of switches, the transfer function of a genetic device, or the oscillations of gene networks. It is rarely possible to know a priori at what times the various changes should be made, and the success of the experiment is unknown until all of the image processing is completed well after the completion of the experiment. This results in wasted time and resources, due to the need to repeat the experiment to fine-tune the imaging parameters. To overcome this limitation, we have developed an adaptive imaging platform called GenoSIGHT that processes images as they are recorded, and uses the resulting data to make real-time adjustments to experimental conditions. We have validated this closed-loop control of the experiment using galactose-inducible expression of the yellow fluorescent protein Venus in Saccharomyces cerevisiae. We show that adaptive imaging improves the reproducibility of gene expression data resulting in more accurate estimates of gene network parameters while increasing productivity ten-fold.

  9. High-resolution imaging of biological tissue with full-field optical coherence tomography

    Science.gov (United States)

    Zhu, Yue; Gao, Wanrong

    2015-03-01

    A new full-field optical coherence tomography system with high-resolution has been developed for imaging of cells and tissues. Compared with other FF-OCT (Full-field optical coherence tomography, FF-OCT) systems illuminated with optical fiber bundle, the improved Köhler illumination arrangement with a halogen lamp was used in the proposed FF-OCT system. High numerical aperture microscopic objectives were used for imaging and a piezoelectric ceramic transducer (PZT) was used for phase-shifting. En-face tomographic images can be obtained by applying the five-step phase-shifting algorithm to a series of interferometric images which are recorded by a smart camera. Three-dimensional images can be generated from these tomographic images. Imaging of the chip of Intel Pentium 4 processor demonstrated the ultrahigh resolution of the system (lateral resolution is 0.8μm ), which approaches the theoretical resolution 0.7 μm× 0.5 μm (lateral × axial). En-face images of cells of onion show an excellent performance of the system in generating en-face images of biological tissues. Then, unstained pig stomach was imaged as a tissue and gastric pits could be easily recognized using FF-OCT system. Our study provides evidence for the potential ability of FFOCT in identifying gastric pits from pig stomach tissue. Finally, label-free and unstained ex vivo human liver tissues from both normal and tumor were imaged with this FFOCT system. The results show that the setup has the potential for medical diagnosis applications such liver cancer diagnosis.

  10. Engineering aspects of the experiment and results of animal tests. [Apollo 17 Biological Cosmic Ray Experiment

    Science.gov (United States)

    Look, B. C.; Tremor, J. W.; Barrows, W. F.; Zabower, H. R.; Suri, K.; Park, E. G., Jr.; Durso, J. A.; Leon, H. A.; Haymaker, W.; Lindberg, R. G.

    1975-01-01

    A closed passive system independent of support from the spacecraft or its crew was developed to house five pocket mice for their flight on Apollo XVII. The reaction of potassium superoxide with carbon dioxide and water vapor to produce oxygen provided a habitable atmosphere within the experiment package. The performance of the system and the ability of the mice to survive the key preflight tests gave reasonable assurance that the mice would also withstand the Apollo flight.-

  11. Detection and Classification of Cancer from Microscopic Biopsy Images Using Clinically Significant and Biologically Interpretable Features

    Science.gov (United States)

    Kumar, Rajesh; Srivastava, Subodh

    2015-01-01

    A framework for automated detection and classification of cancer from microscopic biopsy images using clinically significant and biologically interpretable features is proposed and examined. The various stages involved in the proposed methodology include enhancement of microscopic images, segmentation of background cells, features extraction, and finally the classification. An appropriate and efficient method is employed in each of the design steps of the proposed framework after making a comparative analysis of commonly used method in each category. For highlighting the details of the tissue and structures, the contrast limited adaptive histogram equalization approach is used. For the segmentation of background cells, k-means segmentation algorithm is used because it performs better in comparison to other commonly used segmentation methods. In feature extraction phase, it is proposed to extract various biologically interpretable and clinically significant shapes as well as morphology based features from the segmented images. These include gray level texture features, color based features, color gray level texture features, Law's Texture Energy based features, Tamura's features, and wavelet features. Finally, the K-nearest neighborhood method is used for classification of images into normal and cancerous categories because it is performing better in comparison to other commonly used methods for this application. The performance of the proposed framework is evaluated using well-known parameters for four fundamental tissues (connective, epithelial, muscular, and nervous) of randomly selected 1000 microscopic biopsy images. PMID:27006938

  12. Robust biological parametric mapping: an improved technique for multimodal brain image analysis

    Science.gov (United States)

    Yang, Xue; Beason-Held, Lori; Resnick, Susan M.; Landman, Bennett A.

    2011-03-01

    Mapping the quantitative relationship between structure and function in the human brain is an important and challenging problem. Numerous volumetric, surface, region of interest and voxelwise image processing techniques have been developed to statistically assess potential correlations between imaging and non-imaging metrics. Recently, biological parametric mapping has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. This approach offers great promise for direct, voxelwise assessment of structural and functional relationships with multiple imaging modalities. However, as presented, the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences (e.g., artifactual low p-values) due to slight mis-registration or variation in anatomy between subjects. To enable widespread application of this approach, we introduce robust regression and robust inference in the neuroimaging context of application of the general linear model. Through simulation and empirical studies, we demonstrate that our robust approach reduces sensitivity to outliers without substantial degradation in power. The robust approach and associated software package provides a reliable way to quantitatively assess voxelwise correlations between structural and functional neuroimaging modalities.

  13. Widely tunable, high peak power ultrafast laser sources in biological imaging (Conference Presentation)

    Science.gov (United States)

    Klein, Julien

    2017-02-01

    Widely tunable ultrafast lasers have enabled a large number of biological imaging techniques including point scanning multiphoton excited fluorescence (MPEF), SHG/THG and stimulated Raman imaging. Tunable ultrafast lasers offer spectral agility, covering the entire relative transparency window in live tissue (700-1300nnm) and flexibility with multi-color, synchronized outputs to support sophisticated label free techniques (e.g. stimulated Raman modalities). More recently newly available high peak power lasers based on Ytterbium technology drive advances in two-photon light-sheet, 3 photon excited fluorescence and holographic patterning for optogenetics photo-stimulation. These laser platforms offer a unique blend of compactness, ease of use and cost efficiency, and ideally complement tunable platforms typically based on Ti:Sapphire and IR optical parametric oscillators (OPO). We present various types of ultrafast laser architectures, link their optical characteristics to key bio-imaging requirements, and present relevant examples and images illustrating their impact in biological science. In particular we review the use of ultrafast lasers in optogenetics and fast in-vivo Calcium imaging deep in mouse brain.

  14. [Development of RF coil of permanent magnet mini-magnetic resonance imager and mouse imaging experiments].

    Science.gov (United States)

    Hou, Shulian; Xie, Huantong; Chen, Wei; Wang, Guangxin; Zhao, Qiang; Li, Shiyu

    2014-10-01

    In the development of radio frequency (RF) coils for better quality of the mini-type permanent magnetic resonance imager for using in the small animal imaging, the solenoid RF coil has a special advantage for permanent magnetic system based on analyses of various types.of RF coils. However, it is not satisfied for imaging if the RF coils are directly used. By theoretical analyses of the magnetic field properties produced from the solenoid coil, the research direction was determined by careful studies to raise further the uniformity of the magnetic field coil, receiving coil sensitivity for signals and signal-to-noise ratio (SNR). The method had certain advantages and avoided some shortcomings of the other different coil types, such as, birdcage coil, saddle shaped coil and phased array coil by using the alloy materials (from our own patent). The RF coils were designed, developed and made for keeled applicable to permanent magnet-type magnetic resonance imager, multi-coil combination-type, single-channel overall RF receiving coil, and applied for a patent. Mounted on three instruments (25 mm aperture, with main magnetic field strength of 0.5 T or 1.5 T, and 50 mm aperture, with main magnetic field strength of 0.48 T), we performed experiments with mice, rats, and nude mice bearing tumors. The experimental results indicated that the RF receiving coil was fully applicable to the permanent magnet-type imaging system.

  15. Photothermal Microscopy for High Sensitivity and High Resolution Absorption Contrast Imaging of Biological Tissues

    Directory of Open Access Journals (Sweden)

    Jun Miyazaki

    2017-04-01

    Full Text Available Photothermal microscopy is useful to visualize the distribution of non-fluorescence chromoproteins in biological specimens. Here, we developed a high sensitivity and high resolution photothermal microscopy with low-cost and compact laser diodes as light sources. A new detection scheme for improving signal to noise ratio more than 4-fold is presented. It is demonstrated that spatial resolution in photothermal microscopy is up to nearly twice as high as that in the conventional widefield microscopy. Furthermore, we demonstrated the ability for distinguishing or identifying biological molecules with simultaneous muti-wavelength imaging. Simultaneous photothermal and fluorescence imaging of mouse brain tissue was conducted to visualize both neurons expressing yellow fluorescent protein and endogenous non-fluorescent chromophores.

  16. Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues.

    Science.gov (United States)

    Ji, Na; Milkie, Daniel E; Betzig, Eric

    2010-02-01

    Biological specimens are rife with optical inhomogeneities that seriously degrade imaging performance under all but the most ideal conditions. Measuring and then correcting for these inhomogeneities is the province of adaptive optics. Here we introduce an approach to adaptive optics in microscopy wherein the rear pupil of an objective lens is segmented into subregions, and light is directed individually to each subregion to measure, by image shift, the deflection faced by each group of rays as they emerge from the objective and travel through the specimen toward the focus. Applying our method to two-photon microscopy, we could recover near-diffraction-limited performance from a variety of biological and nonbiological samples exhibiting aberrations large or small and smoothly varying or abruptly changing. In particular, results from fixed mouse cortical slices illustrate our ability to improve signal and resolution to depths of 400 microm.

  17. Cerenkov radiation energy transfer (CRET imaging: a novel method for optical imaging of PET isotopes in biological systems.

    Directory of Open Access Journals (Sweden)

    Robin S Dothager

    Full Text Available BACKGROUND: Positron emission tomography (PET allows sensitive, non-invasive analysis of the distribution of radiopharmaceutical tracers labeled with positron (β(+-emitting radionuclides in small animals and humans. Upon β(+ decay, the initial velocity of high-energy β(+ particles can momentarily exceed the speed of light in tissue, producing Cerenkov radiation that is detectable by optical imaging, but is highly absorbed in living organisms. PRINCIPAL FINDINGS: To improve optical imaging of Cerenkov radiation in biological systems, we demonstrate that Cerenkov radiation from decay of the PET isotopes (64Cu and (18F can be spectrally coupled by energy transfer to high Stokes-shift quantum nanoparticles (Qtracker705 to produce highly red-shifted photonic emissions. Efficient energy transfer was not detected with (99mTc, a predominantly γ-emitting isotope. Similar to bioluminescence resonance energy transfer (BRET and fluorescence resonance energy transfer (FRET, herein we define the Cerenkov radiation energy transfer (CRET ratio as the normalized quotient of light detected within a spectral window centered on the fluorophore emission divided by light detected within a spectral window of the Cerenkov radiation emission to quantify imaging signals. Optical images of solutions containing Qtracker705 nanoparticles and [(18F]FDG showed CRET ratios in vitro as high as 8.8±1.1, while images of mice with subcutaneous pseudotumors impregnated with Qtracker705 following intravenous injection of [(18F]FDG showed CRET ratios in vivo as high as 3.5±0.3. CONCLUSIONS: Quantitative CRET imaging may afford a variety of novel optical imaging applications and activation strategies for PET radiopharmaceuticals and other isotopes in biomaterials, tissues and live animals.

  18. Third order harmonic imaging for biological tissues using three phase-coded pulses.

    Science.gov (United States)

    Ma, Qingyu; Gong, Xiufen; Zhang, Dong

    2006-12-22

    Compared to the fundamental and the second harmonic imaging, the third harmonic imaging shows significant improvements in image quality due to the better resolution, but it is degraded by the lower sound pressure and signal-to-noise ratio (SNR). In this study, a phase-coded pulse technique is proposed to selectively enhance the sound pressure of the third harmonic by 9.5 dB whereas the fundamental and the second harmonic components are efficiently suppressed and SNR is also increased by 4.7 dB. Based on the solution of the KZK nonlinear equation, the axial and lateral beam profiles of harmonics radiated from a planar piston transducer were theoretically simulated and experimentally examined. Finally, the third harmonic images using this technique were performed for several biological tissues and compared with the images obtained by the fundamental and the second harmonic imaging. Results demonstrate that the phase-coded pulse technique yields a dramatically cleaner and sharper contrast image.

  19. Biologically relevant photoacoustic imaging phantoms with tunable optical and acoustic properties

    Science.gov (United States)

    Vogt, William C.; Jia, Congxian; Wear, Keith A.; Garra, Brian S.; Joshua Pfefer, T.

    2016-10-01

    Established medical imaging technologies such as magnetic resonance imaging and computed tomography rely on well-validated tissue-simulating phantoms for standardized testing of device image quality. The availability of high-quality phantoms for optical-acoustic diagnostics such as photoacoustic tomography (PAT) will facilitate standardization and clinical translation of these emerging approaches. Materials used in prior PAT phantoms do not provide a suitable combination of long-term stability and realistic acoustic and optical properties. Therefore, we have investigated the use of custom polyvinyl chloride plastisol (PVCP) formulations for imaging phantoms and identified a dual-plasticizer approach that provides biologically relevant ranges of relevant properties. Speed of sound and acoustic attenuation were determined over a frequency range of 4 to 9 MHz and optical absorption and scattering over a wavelength range of 400 to 1100 nm. We present characterization of several PVCP formulations, including one designed to mimic breast tissue. This material is used to construct a phantom comprised of an array of cylindrical, hemoglobin-filled inclusions for evaluation of penetration depth. Measurements with a custom near-infrared PAT imager provide quantitative and qualitative comparisons of phantom and tissue images. Results indicate that our PVCP material is uniquely suitable for PAT system image quality evaluation and may provide a practical tool for device validation and intercomparison.

  20. In Vivo Bioluminescent Imaging (BLI): Noninvasive Visualization and Interrogation of Biological Processes in Living Animals

    OpenAIRE

    Steven Ripp; Sayler, Gary S.; Tingting Xu; Close, Dan M.

    2010-01-01

    In vivo bioluminescent imaging (BLI) is increasingly being utilized as a method for modern biological research. This process, which involves the noninvasive interrogation of living animals using light emitted from luciferase-expressing bioreporter cells, has been applied to study a wide range of biomolecular functions such as gene function, drug discovery and development, cellular trafficking, protein-protein interactions, and especially tumorigenesis, cancer treatment, and disease progressio...

  1. High-Magnification In Vivo Imaging of Xenopus Embryos for Cell and Developmental Biology

    OpenAIRE

    sprotocols

    2014-01-01

    Authors: Esther K. Kieserman, Chanjae Lee, Ryan S. Gray, Tae Joo Park and John B. Wallingford Corresponding author ([]()). ### INTRODUCTION Embryos of the frog *Xenopus laevis* are an ideal model system for in vivo imaging of dynamic biological processes, from the inner workings of individual cells to the reshaping of tissues during embryogenesis. Their externally developing embryos are more amenable to in vivo analysis than in...

  2. Multi-energy method of digital radiography for imaging of biological objects

    Science.gov (United States)

    Ryzhikov, V. D.; Naydenov, S. V.; Opolonin, O. D.; Volkov, V. G.; Smith, C. F.

    2016-03-01

    This work has been dedicated to the search for a new possibility to use multi-energy digital radiography (MER) for medical applications. Our work has included both theoretical and experimental investigations of 2-energy (2E) and 3- energy (3D) radiography for imaging the structure of biological objects. Using special simulation methods and digital analysis based on the X-ray interaction energy dependence for each element of importance to medical applications in the X-ray range of energy up to 150 keV, we have implemented a quasi-linear approximation for the energy dependence of the X-ray linear mass absorption coefficient μm (E) that permits us to determine the intrinsic structure of the biological objects. Our measurements utilize multiple X-ray tube voltages (50, 100, and 150 kV) with Al and Cu filters of different thicknesses to achieve 3-energy X-ray examination of objects. By doing so, we are able to achieve significantly improved imaging quality of the structure of the subject biological objects. To reconstruct and visualize the final images, we use both two-dimensional (2D) and three-dimensional (3D) palettes of identification. The result is a 2E and/or 3E representation of the object with color coding of each pixel according to the data outputs. Following the experimental measurements and post-processing, we produce a 3D image of the biological object - in the case of our trials, fragments or parts of chicken and turkey.

  3. Polarization-sensitive optical coherence tomography for imaging of biological tissues

    Science.gov (United States)

    Chen, Xiaodong; Wang, Yi; Li, Wanhui; Yu, Daoyin

    2006-09-01

    Polarization sensitive optical coherence tomography (PS-OCT) is a new non-contact and non-invasive method for measuring the change of birefringence in biological tissues caused by pathological changes of body. It has great potential in imaging the structural properties of turbid biological media because the polarization state of light backscattered from biological tissues is influenced by the birefringence of fibrous structures. The arrangement is based on a Michelson interferometer with use of quarter-wave plates and polarimeter. Through the detection of light backscattered from biological tissues and reflected from a reference mirror, the optical phase delay between orthogonal polarization compositions propagating in the birefringence media can be measured. PS-OCT is a powerful tool for research of tendon, dentin, lesions, which have strong polarization effective. We in this paper describe the experimental scheme and its mathematical representation, along with the theory of PS-OCT imaging. Besides, we introduce a fiber-based PS-OCT system for measuring the tissue birefringence.

  4. Feature point tracking and trajectory analysis for video imaging in cell biology.

    Science.gov (United States)

    Sbalzarini, I F; Koumoutsakos, P

    2005-08-01

    This paper presents a computationally efficient, two-dimensional, feature point tracking algorithm for the automated detection and quantitative analysis of particle trajectories as recorded by video imaging in cell biology. The tracking process requires no a priori mathematical modeling of the motion, it is self-initializing, it discriminates spurious detections, and it can handle temporary occlusion as well as particle appearance and disappearance from the image region. The efficiency of the algorithm is validated on synthetic video data where it is compared to existing methods and its accuracy and precision are assessed for a wide range of signal-to-noise ratios. The algorithm is well suited for video imaging in cell biology relying on low-intensity fluorescence microscopy. Its applicability is demonstrated in three case studies involving transport of low-density lipoproteins in endosomes, motion of fluorescently labeled Adenovirus-2 particles along microtubules, and tracking of quantum dots on the plasma membrane of live cells. The present automated tracking process enables the quantification of dispersive processes in cell biology using techniques such as moment scaling spectra.

  5. The combination of pulsed acousto-optic imaging and B-mode diagnostic ultrasound for three-dimensional imaging in ex vivo biological tissue

    Science.gov (United States)

    Sui, Lei; Murray, Todd W.; Roy, Ronald A.

    2006-02-01

    A multimode imaging system, producing conventional ultrasound (US) and acousto-optic (AO) images, has been developed and used to detect optical absorbers buried in excised biological tissue. A commercially-available diagnostic ultrasound imaging transducer is used to both generate B-mode ultrasound images and as a pump for AO imaging. Due to the fact that the steered and focused beam used for US imaging and the US source for pumping the AO image are generated from the same ultrasound probe, the acoustical and optical images are intrinsically co-registered. AO imaging is performed using short ultrasound pulse trains at a frequency of 5 MHz. The phase-modulated light emitted from the interaction region is detected using a photorefractive-crystal based interferometry system. Experimental results have previously been presented for the two-dimensional imaging in tissue-mimicking phantoms. In this paper, we report further experimental developments demonstrating three-dimensional fusion of B-mode ultrasound imaging and pulsed acousto-optic imaging in excised biological tissue (~2 cm thick). By mechanically scanning the ultrasound transducer array in a direction perpendicular to its imaging plane, both the acoustical and optical properties of an embedded target are obtained in three dimensions. The results suggest that AO imaging could be used to supplement conventional B-mode ultrasound imaging with optical contrast, and the multimode imaging system may find application in the detection and diagnosis of cancer.

  6. A robust co-localisation measurement utilising z-stack image intensity similarities for biological studies.

    Directory of Open Access Journals (Sweden)

    Yinhai Wang

    Full Text Available BACKGROUND: Co-localisation is a widely used measurement in immunohistochemical analysis to determine if fluorescently labelled biological entities, such as cells, proteins or molecules share a same location. However the measurement of co-localisation is challenging due to the complex nature of such fluorescent images, especially when multiple focal planes are captured. The current state-of-art co-localisation measurements of 3-dimensional (3D image stacks are biased by noise and cross-overs from non-consecutive planes. METHOD: In this study, we have developed Co-localisation Intensity Coefficients (CICs and Co-localisation Binary Coefficients (CBCs, which uses rich z-stack data from neighbouring focal planes to identify similarities between image intensities of two and potentially more fluorescently-labelled biological entities. This was developed using z-stack images from murine organotypic slice cultures from central nervous system tissue, and two sets of pseudo-data. A large amount of non-specific cross-over situations are excluded using this method. This proposed method is also proven to be robust in recognising co-localisations even when images are polluted with a range of noises. RESULTS: The proposed CBCs and CICs produce robust co-localisation measurements which are easy to interpret, resilient to noise and capable of removing a large amount of false positivity, such as non-specific cross-overs. Performance of this method of measurement is significantly more accurate than existing measurements, as determined statistically using pseudo datasets of known values. This method provides an important and reliable tool for fluorescent 3D neurobiological studies, and will benefit other biological studies which measure fluorescence co-localisation in 3D.

  7. The Ring Imaging Cherenkov detector (RICH) of the AMS experiment

    CERN Document Server

    Barão, F; Alcaraz, J; Arruda, L; Barrau, A; Barreira, G; Belmont, E; Berdugo, J; Brinet, M; Buénerd, M; Casadei, D; Casaus, J; Cortina, E; Delgado, C; Díaz, C; Derome, L; Eraud, L; Garcia-Lopez, R J; Gallin-Martel, L; Giovacchini, F; Gonçalves, P; Lanciotti, E; Laurenti, G; Malinine, A; Maña, C; Marin, J; Martínez, G; Menchaca-Rocha, A; Molla, M; Palomares, C; Panniello, M; Pereira, R; Pimenta, M; Protasov, K; Sánchez, E; Seo, E S; Sevilla, N; Torrento, A; Vargas-Trevino, M; Veziant, O

    2006-01-01

    The Alpha Magnetic Spectrometer (AMS) experiment to be installed on the International Space Station (ISS) will be equipped with a proximity focusing Ring Imaging Cherenkov (RICH) detector for measuring the electric charge and velocity of the charged cosmic particles. A RICH prototype consisting of 96 photomultiplier units, including a piece of the conical reflector, was built and its performance evaluated with ion beam data. Preliminary results of the in-beam tests performed with ion fragments resulting from collisions of a 158 GeV/c/nuc primary beam of Indium ions (CERN SPS) on a Pb target are reported. The collected data included tests to the final front-end electronics and to different aerogel radiators. Cherenkov rings for a large range of charged nuclei and with reflected photons were observed. The data analysis confirms the design goals. Charge separation up to Fe and velocity resolution of the order of 0.1% for singly charged particles are obtained.

  8. A Feedfordward Adaptive Controller to Reduce the Imaging Time of Large-Sized Biological Samples with a SPM-Based Multiprobe Station

    Directory of Open Access Journals (Sweden)

    Manel Puig-Vidal

    2012-01-01

    Full Text Available The time required to image large samples is an important limiting factor in SPM-based systems. In multiprobe setups, especially when working with biological samples, this drawback can make impossible to conduct certain experiments. In this work, we present a feedfordward controller based on bang-bang and adaptive controls. The controls are based in the difference between the maximum speeds that can be used for imaging depending on the flatness of the sample zone. Topographic images of Escherichia coli bacteria samples were acquired using the implemented controllers. Results show that to go faster in the flat zones, rather than using a constant scanning speed for the whole image, speeds up the imaging process of large samples by up to a 4x factor.

  9. Chemical Biology in the Embryo: In Situ Imaging of Sulfur Biochemistry in Normal and Proteoglycan-Deficient Cartilage Matrix.

    Science.gov (United States)

    Hackett, Mark J; George, Graham N; Pickering, Ingrid J; Eames, B Frank

    2016-05-01

    Proteoglycans (PGs) are heavily glycosylated proteins that play major structural and biological roles in many tissues. Proteoglycans are abundant in cartilage extracellular matrix; their loss is a main feature of the joint disease osteoarthritis. Proteoglycan function is regulated by sulfation-sulfate ester formation with specific sugar residues. Visualization of sulfation within cartilage matrix would yield vital insights into its biological roles. We present synchrotron-based X-ray fluorescence imaging of developing zebrafish cartilage, providing the first in situ maps of sulfate ester distribution. Levels of both sulfur and sulfate esters decrease as cartilage develops through late phase differentiation (maturation or hypertrophy), suggesting a functional link between cartilage matrix sulfur content and chondrocyte differentiation. Genetic experiments confirm that sulfate ester levels were due to cartilage proteoglycans and support the hypothesis that sulfate ester levels regulate chondrocyte differentiation. Surprisingly, in the PG synthesis mutant, the total level of sulfur was not significantly reduced, suggesting sulfur is distributed in an alternative chemical form during lowered cartilage proteoglycan production. Fourier transform infrared imaging indicated increased levels of protein in the mutant fish, suggesting that this alternative sulfur form might be ascribed to an increased level of protein synthesis in the mutant fish, as part of a compensatory mechanism.

  10. Pixel Perfect: a real-time image processing system for biology

    Energy Technology Data Exchange (ETDEWEB)

    Perrine, Kenneth A.; Hopkins, Derek F.; Lamarche, Brian L.; Budge, Scott E.; Sowa, Marianne B.

    2005-09-16

    Scientific visioning systems often rely upon pixel-perfect precision to produce meaningful data. Cutting-edge equipment used in the study of cell signaling is no exception; proper image alignment is critical for successful experiments. Biologists at Pacific Northwest National Laboratory put together a special multi-spectral confocal microscope that was capable of producing live images of cells and proteins in two simultaneous spectral channels. But there was a problem: the dual images resembled poorly registered Sunday comics and were unusable. This article describes how the biologists worked with programmers to fix the difficulty and make the microscope a truly useful and unique device.

  11. TESIS experiment on EUV imaging spectroscopy of the Sun

    Science.gov (United States)

    Kuzin, S. V.; Bogachev, S. A.; Zhitnik, I. A.; Pertsov, A. A.; Ignatiev, A. P.; Mitrofanov, A. M.; Slemzin, V. A.; Shestov, S. V.; Sukhodrev, N. K.; Bugaenko, O. I.

    2009-03-01

    TESIS is a set of solar imaging instruments in development by the Lebedev Physical Institute of the Russian Academy of Science, to be launched aboard the Russian spacecraft CORONAS-PHOTON in December 2008. The main goal of TESIS is to provide complex observations of solar active phenomena from the transition region to the inner and outer solar corona with high spatial, spectral and temporal resolution in the EUV and Soft X-ray spectral bands. TESIS includes five unique space instruments: the MgXII Imaging Spectroheliometer (MISH) with spherical bent crystal mirror, for observations of the Sun in the monochromatic MgXII 8.42 Å line; the EUV Spectoheliometer (EUSH) with grazing incidence difraction grating, for the registration of the full solar disc in monochromatic lines of the spectral band 280-330 Å; two Full-disk EUV Telescopes (FET) with multilayer mirrors covering the band 130-136 and 290-320 Å; and the Solar EUV Coronagraph (SEC), based on the Ritchey-Chretien scheme, to observe the inner and outer solar corona from 0.2 to 4 solar radii in spectral band 290-320 Å. TESIS experiment will start at the rising phase of the 24th cycle of solar activity. With the advanced capabilities of its instruments, TESIS will help better understand the physics of solar flares and high-energy phenomena and provide new data on parameters of solar plasma in the temperature range 10-10K. This paper gives a brief description of the experiment, its equipment, and its scientific objectives.

  12. Molecular Imaging of Biological Gene Delivery Vehicles for Targeted Cancer Therapy: Beyond Viral Vectors

    Energy Technology Data Exchange (ETDEWEB)

    Min, Jung Joon; Nguyen, Vu H. [Chonnam National University Medical School, Gwangju (Korea, Republic of); Gambhir, Sanjiv S. [Stanford University, California(United States)

    2010-04-15

    Cancer persists as one of the most devastating diseases in the world. Problems including metastasis and tumor resistance to chemotherapy and radiotherapy have seriously limited the therapeutic effects of present clinical treatments. To overcome these limitations, cancer gene therapy has been developed over the last two decades for a broad spectrum of applications, from gene replacement and knockdown to vaccination, each with different requirements for gene delivery. So far, a number of genes and delivery vectors have been investigated, and significant progress has been made with several gene therapy modalities in clinical trials. Viral vectors and synthetic liposomes have emerged as the vehicles of choice for many applications. However, both have limitations and risks that restrict gene therapy applications, including the complexity of production, limited packaging capacity, and unfavorable immunological features. While continuing to improve these vectors, it is important to investigate other options, particularly nonarrival biological agents such as bacteria, bacteriophages, and bacteria-like particles. Recently, many molecular imaging techniques for safe, repeated, and high-resolution in vivo imaging of gene expression have been employed to assess vector-mediated gene expression in living subjects. In this review, molecular imaging techniques for monitoring biological gene delivery vehicles are described, and the specific use of these methods at different steps is illustrated. Linking molecular imaging to gene therapy will eventually help to develop novel gene delivery vehicles for preclinical study and support the development of future human applications.

  13. Handheld hyperspectral imager for standoff detection of chemical and biological aerosols

    Science.gov (United States)

    Hinnrichs, Michele; Jensen, James O.; McAnally, Gerard

    2004-08-01

    Pacific Advanced Technology has developed a small hand held imaging spectrometer, Sherlock, for gas leak and aerosol detection and imaging. The system is based on a patented technique, (IMSS Image Multi-spectral Sensing), that uses diffractive optics and image processing algorithms to detect spectral information about objects in the scene of the camera. This cameras technology has been tested at Dugway Proving Ground and Dstl Porton Down facilities looking at Chemical and Biological agent simulants. In addition to Chemical and Biological detection, the camera has been used for environmental monitoring of green house gases and is currently undergoing extensive laboratory and field testing by the Gas Technology Institute, British Petroleum and Shell Oil for applications for gas leak detection and repair. In this paper we will present some of the results from the data collection at the TRE test at Dugway Proving Ground during the summer of 2002 and laboratory testing at the Dstl facility at Porton Down in the UK in the fall of 2002.

  14. Design of a Comprehensive Biochemistry and Molecular Biology Experiment: Phase Variation Caused by Recombinational Regulation of Bacterial Gene Expression

    Science.gov (United States)

    Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

    2014-01-01

    Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about "Salmonella enterica" serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation,…

  15. XperimentR: painless annotation of a biological experiment for the laboratory scientist

    Directory of Open Access Journals (Sweden)

    Tomlinson Chris D

    2013-01-01

    Full Text Available Abstract Background Today’s biological experiments often involve the collaboration of multidisciplinary researchers utilising several high throughput ‘omics platforms. There is a requirement for the details of the experiment to be adequately described using standardised ontologies to enable data preservation, the analysis of the data and to facilitate the export of the data to public repositories. However there are a bewildering number of ontologies, controlled vocabularies, and minimum standards available for use to describe experiments. There is a need for user-friendly software tools to aid laboratory scientists in capturing the experimental information. Results A web application called XperimentR has been developed for use by laboratory scientists, consisting of a browser-based interface and server-side components which provide an intuitive platform for capturing and sharing experimental metadata. Information recorded includes details about the biological samples, procedures, protocols, and experimental technologies, all of which can be easily annotated using the appropriate ontologies. Files and raw data can be imported and associated with the biological samples via the interface, from either users’ computers, or commonly used open-source data repositories. Experiments can be shared with other users, and experiments can be exported in the standard ISA-Tab format for deposition in public databases. XperimentR is freely available and can be installed natively or by using a provided pre-configured Virtual Machine. A guest system is also available for trial purposes. Conclusion We present a web based software application to aid the laboratory scientist to capture, describe and share details about their experiments.

  16. A numerical method for imaging of biological microstructures by VHF waves

    CERN Document Server

    Ala, Guido; Francomano, Elisa; Ganci, Salvatore

    2013-01-01

    Imaging techniques give a fundamental support to medical diagnostics during the pathology discovery as well as for the characterization of biological structures. The imaging methods involve electromagnetic waves in a frequency range that spans from some Hz to GHz and over. Most of these methods involve scanning of wide human body areas even if only small areas need to be analyzed. In this paper, a numerical method to evaluate the shape of micro-structures for application in the medical ?field, with a very low invasiveness for the human body, is proposed. A flexible thin-wire antenna radiates the VHF waves and then, by measuring the spatial magnetic ?field distribution it is possible to reconstruct the micro-structures image by estimating the location of the antenna against a sensors panel. The typical inverse problem described above is solved numerically, and ?first simulation results are presented in order to show the validity and the robustness of the proposed approach.

  17. 3D Imaging of Nanoparticle Distribution in Biological Tissue by Laser-Induced Breakdown Spectroscopy

    Science.gov (United States)

    Gimenez, Y.; Busser, B.; Trichard, F.; Kulesza, A.; Laurent, J. M.; Zaun, V.; Lux, F.; Benoit, J. M.; Panczer, G.; Dugourd, P.; Tillement, O.; Pelascini, F.; Sancey, L.; Motto-Ros, V.

    2016-07-01

    Nanomaterials represent a rapidly expanding area of research with huge potential for future medical applications. Nanotechnology indeed promises to revolutionize diagnostics, drug delivery, gene therapy, and many other areas of research. For any biological investigation involving nanomaterials, it is crucial to study the behavior of such nano-objects within tissues to evaluate both their efficacy and their toxicity. Here, we provide the first account of 3D label-free nanoparticle imaging at the entire-organ scale. The technology used is known as laser-induced breakdown spectroscopy (LIBS) and possesses several advantages such as speed of operation, ease of use and full compatibility with optical microscopy. We then used two different but complementary approaches to achieve 3D elemental imaging with LIBS: a volume reconstruction of a sliced organ and in-depth analysis. This proof-of-concept study demonstrates the quantitative imaging of both endogenous and exogenous elements within entire organs and paves the way for innumerable applications.

  18. Pushing the physical limits of spectroscopic imaging for new biology and better medicine (Conference Presentation)

    Science.gov (United States)

    Cheng, Ji-Xin

    2017-02-01

    In vivo molecular spectroscopic imaging is not a simple addition of a spectrometer to a microscope. Innovations are needed to break the physical limits in sensitivity, depth, speed and resolution perspectives. I will present our most recent advances in modality development, biological application, and clinical translation. My talk will focus on the development of mid-infrared photothermal microscope for depth-resolved vibrational imaging of living cells (Science Advances, in press), the discovery of a metabolic signature in cancer stem cells by hyperspectral stimulated Raman scattering imaging (Cell Stem Cell, in press), and the development of an intravascular vibrational photoacoustic catheter for label-free sensing of lipid laden plaques (Scientific Report 2016, 6:25236).

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

    Science.gov (United States)

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

    2017-02-01

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

  20. Development of ring imaging Cherenkov detectors for the LHCb experiment

    CERN Document Server

    John, M J J

    2001-01-01

    This thesis reports on work done as part of the development of the Ring Imaging Cherenkov (RICH) detectors of the LHCb experiment. The context of this work is set out in Chapter 1, which includes an overview of the physics of CP violation, followed by a discussion of other experiments that study B physics. LHCb itself is then described, with particular emphasis on its RICH detectors, and the photon detectors to be used therein. The work done by the author to ensure an adequate shielding of the photon detectors in the two RICH detectors from the magnetic fields produced by the LHCb dipole is then presented. A candidate photodetector for the RICH is the Pixel HPD. The author's contribution to the upgrade of the HPD test system to operate at the LHC bunch-crossing rate of 40MHz is the subject of the following section. This system was used to investigate and optimise a method of minimising the threshold distribution of the Pixel HPD's encapsulated readout chip. The final chapter of the thesis concerns the aerogel...

  1. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  2. Synthesis, biological evaluation, and live cell imaging of novel fluorescent duocarmycin analogs.

    Science.gov (United States)

    Tietze, Lutz F; Behrendt, Frank; Pestel, Galina F; Schuberth, Ingrid; Mitkovski, Mišo

    2012-11-01

    For a better understanding of the mode of action of duocarmycin and its analogs, the novel fluorescent duocarmycin derivatives 13-15 and 17b-19b were synthesized, and their bioactivity as well as their cellular uptake investigated using confocal laser scanning microscopy (CLSM) in live-cell imaging experiments. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

  3. Impact of ultrafast electronic damage in single particle x-ray imaging experiments

    CERN Document Server

    Lorenz, U; Weckert, E; Vartanyants, I A

    2012-01-01

    In single particle coherent x-ray diffraction imaging experiments, performed at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray pulses to obtain single-shot diffraction patterns. The high intensity induces electronic dynamics on the femtosecond time scale in the system, which can reduce the contrast of the obtained diffraction patterns and adds an isotropic background. We quantify the degradation of the diffraction pattern from ultrafast electronic damage by performing simulations on a biological sample exposed to x-ray pulses with different parameters. We find that the contrast is substantially reduced and the background is considerably strong only if almost all electrons are removed from their parent atoms. This happens at fluences of at least one order of magnitude larger than provided at currently available XFEL sources.

  4. Impact of ultrafast electronic damage in single-particle x-ray imaging experiments

    Science.gov (United States)

    Lorenz, U.; Kabachnik, N. M.; Weckert, E.; Vartanyants, I. A.

    2012-11-01

    In single-particle coherent x-ray diffraction imaging experiments, performed at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray pulses to obtain single-shot diffraction patterns. The high intensity induces electronic dynamics on the femtosecond time scale in the system, which can reduce the contrast of the obtained diffraction patterns and adds an isotropic background. We quantify the degradation of the diffraction pattern from ultrafast electronic damage by performing simulations on a biological sample exposed to x-ray pulses with different parameters. We find that the contrast is substantially reduced and the background is considerably strong only if almost all electrons are removed from their parent atoms. This happens at fluences of at least one order of magnitude larger than provided at currently available XFEL sources.

  5. FEM-based simulation of a fluorescence tomography experiment using anatomical MR images

    Science.gov (United States)

    Ren, Wuwei; Elmer, Andreas; Augath, Mark-Aurel; Rudin, Markus

    2016-03-01

    A hybrid system combining fluorescence molecular tomography (FMT) and magnetic resonance imaging (MRI) is attractive for preclinical imaging as it allows fusion of molecular information derived from FMT and anatomical reference data derived from MRI. We have previously developed such a system and demonstrated its performance in biological applications. For reconstruction slab geometry with homogeneous optical parameters was assumed, which led to undesirable artifacts. In order to exploit the power of the hybrid system, the use of MRI derived anatomical information, as a constraint for FMT reconstruction, appears logical. Heterogeneity of tissues and irregular surface derived from MRI can be accounted for by generating a mesh using the finite element method (FEM), and attributing optical parameters to individual mesh points. We have established a forward simulation tool based on TOAST++ to mimic an FMT experiment. MRI images were recorded on a 9.4T MR scanner using a T1-weighted pulse sequence. The voxelized dataset was processed by iso2mesh to yield a 3D-mesh. Four steps of FMT simulation were included: 1) Assignment of optical properties, 2) Specification of boundary conditions and generation of 3) excitation and 4) emission maps. FEM-derived results were compared with those obtained using the analytical solution of Green's function and with experimental data with a single fluorescent inclusion in a silicon phantom. Once, the forward modeling method is properly validated it will be used as a central element of a reconstruction algorithm for analyzing data derived from a hybrid FMT/MRI setup.

  6. Non-contact, ultrasound-based indentation method for measuring elastic properties of biological tissues using harmonic motion imaging (HMI).

    Science.gov (United States)

    Vappou, Jonathan; Hou, Gary Y; Marquet, Fabrice; Shahmirzadi, Danial; Grondin, Julien; Konofagou, Elisa E

    2015-04-07

    Noninvasive measurement of mechanical properties of biological tissues in vivo could play a significant role in improving the current understanding of tissue biomechanics. In this study, we propose a method for measuring elastic properties non-invasively by using internal indentation as generated by harmonic motion imaging (HMI). In HMI, an oscillating acoustic radiation force is produced by a focused ultrasound transducer at the focal region, and the resulting displacements are estimated by tracking radiofrequency signals acquired by an imaging transducer. In this study, the focal spot region was modeled as a rigid cylindrical piston that exerts an oscillatory, uniform internal force to the underlying tissue. The HMI elastic modulus EHMI was defined as the ratio of the applied force to the axial strain measured by 1D ultrasound imaging. The accuracy and the precision of the EHMI estimate were assessed both numerically and experimentally in polyacrylamide tissue-mimicking phantoms. Initial feasibility of this method in soft tissues was also shown in canine liver specimens in vitro. Very good correlation and agreement was found between the measured Young's modulus and the HMI modulus in the numerical study (r(2) > 0.99, relative error tissues at a submillimeter scale using an internal indentation-like approach. Ongoing studies include in vitro experiments in a larger number of samples and feasibility testing in in vivo models as well as pathological human specimens.

  7. Full-field quantitative phase imaging by white-light interferometry with active phase stabilization and its application to biological samples

    Science.gov (United States)

    Li, Xinhong; Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka; Zhang, Haijun; Hiruma, Teruo

    2006-06-01

    We report a Koehler-illumination-based full-field, actively stabilized, low-coherence phase-shifting interferometer, which is built on a white-light Michelson interferometer. By using a phase-stepping technique we can obtain full-field phase images of the sample. An actively stabilized phase-lock circuit is employed in the system to reduce phase noise. An application to human epithelial cells (HeLa cells) is achieved in our experiment. The advancement of this technique rests in its ability to take images of unstained biological samples quantitatively and on a nanometer scale.

  8. The Sun Radio Imaging Space Experiment (SunRISE) Mission

    Science.gov (United States)

    Lazio, Joseph; Kasper, Justin; Maksimovic, Milan; Alibay, Farah; Amiri, Nikta; Bastian, Tim; Cohen, Christina; Landi, Enrico; Manchester, Ward; Reinard, Alysha; Schwadron, Nathan; Cecconi, Baptiste; Hallinan, Gregg; Hegedus, Alex; Krupar, Vratislav; Zaslavsky, Arnaud

    2017-04-01

    Radio emission from coronal mass ejections (CMEs) is a direct tracer of particle acceleration in the inner heliosphere and potential magnetic connections from the lower solar corona to the larger heliosphere. Energized electrons excite Langmuir waves, which then convert into intense radio emission at the local plasma frequency, with the most intense acceleration thought to occur within 20 RS. The radio emission from CMEs is quite strong such that only a relatively small number of antennas is required to detect and map it, but many aspects of this particle acceleration and transport remain poorly constrained. Ground-based arrays would be quite capable of tracking the radio emission associated with CMEs, but absorption by the Earth's ionosphere limits the frequency coverage of ground-based arrays (ν ≳ 15 MHz), which in turn limits the range of solar distances over which they can track the radio emission (≲ 3RS). The state-of-the-art for tracking such emission from space is defined by single antennas (Wind/WAVES, Stereo/SWAVES), in which the tracking is accomplished by assuming a frequency-to-density mapping; there has been some success in triangulating the emission between the spacecraft, but considerable uncertainties remain. We describe the Sun Radio Imaging Space Experiment (SunRISE) mission concept: A constellation of small spacecraft in a geostationary graveyard orbit designed to localize and track radio emissions in the inner heliosphere. Each spacecraft would carry a receiving system for observations below 25 MHz, and SunRISE would produce the first images of CMEs more than a few solar radii from the Sun. Part of this research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration.

  9. Value or waste: Perfusion imaging following radiofrequency ablation - early experience.

    Science.gov (United States)

    Thieme, Stefan F; Vahldiek, Janis L; Tummler, Katja; Poch, Franz; Gemeinhardt, Ole; Hiebl, Bernhard; Lehmann, Kai S; Hamm, B; Niehues, Stefan M

    2015-01-01

    Radiofrequency ablation (RFA) is an evolving technique in treatment of hepatic malignant tumors. By heating local tissue it leads to coagulative necrotic areas around the ablation probe. Temperature falls with increasing distance to the probe, risking incomplete necrosis at the margins of the RFA-induced lesion. Therefore, immediate non-invasive and precise detection of incomplete ablation is necessary for early enlargement of the ablation if needed. This in vivo pig study compares early experiences of immediate post-interventional computed tomography (CT) perfusion volume analysis to macroscopic and CT image evaluation in healthy pig liver. RFA was performed in vivo in healthy pig livers. Different CT perfusion algorithms (Maximum slope analysis and Patlak plot) were used to quantify three different perfusion parameters. Data points were acquired from rectangular grids. These grids were semiautomatically overlayed to macroscopic images documented after liver explantation. Each data point was visually assigned to zones defined as "inner" and "outer necrotic zone", "margin" or "vital tissue". Significant differences between necrotic zones and vital tissue are shown for equivalent blood volume (p <  0.0001), arterial flow (p <  0.01) and flow extraction product (p <  0.001). Looking at equivalent blood volume and flow extraction product, there were also significant differences (EquivBV: p <  0.0001, FE: p <  0.001) between margins, necrotic and vital areas. In a porcine model these early results could show that all of the used CT perfusion parameters allowed discrimination of necrosis from vital tissue after RFA at high levels of significance. In addition, the parameters EquivBV and FE that give an estimate of the tissue blood volume and the permeability, were able to precisely discern different zones also seen macroscopically. From this data CT perfusion analysis could be precise tool for measurement and visualization of ablated liver lesions and

  10. Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope

    Science.gov (United States)

    Wu, J.S.; Kim, A. M.; Bleher, R.; Myers, B.D.; Marvin, R. G.; Inada, H.; Nakamura, K.; Zhang, X.F.; Roth, E.; Li, S.Y.; Woodruff, T. K.; O'Halloran, T. V.; Dravid, Vinayak P.

    2013-01-01

    A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room- and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. PMID:23500508

  11. Optimal experiment selection for parameter estimation in biological differential equation models

    Directory of Open Access Journals (Sweden)

    Transtrum Mark K

    2012-07-01

    Full Text Available Abstract Background Parameter estimation in biological models is a common yet challenging problem. In this work we explore the problem for gene regulatory networks modeled by differential equations with unknown parameters, such as decay rates, reaction rates, Michaelis-Menten constants, and Hill coefficients. We explore the question to what extent parameters can be efficiently estimated by appropriate experimental selection. Results A minimization formulation is used to find the parameter values that best fit the experiment data. When the data is insufficient, the minimization problem often has many local minima that fit the data reasonably well. We show that selecting a new experiment based on the local Fisher Information of one local minimum generates additional data that allows one to successfully discriminate among the many local minima. The parameters can be estimated to high accuracy by iteratively performing minimization and experiment selection. We show that the experiment choices are roughly independent of which local minima is used to calculate the local Fisher Information. Conclusions We show that by an appropriate choice of experiments, one can, in principle, efficiently and accurately estimate all the parameters of gene regulatory network. In addition, we demonstrate that appropriate experiment selection can also allow one to restrict model predictions without constraining the parameters using many fewer experiments. We suggest that predicting model behaviors and inferring parameters represent two different approaches to model calibration with different requirements on data and experimental cost.

  12. Molecular imaging of prostate cancer: translating molecular biology approaches into the clinical realm

    Energy Technology Data Exchange (ETDEWEB)

    Vargas, Hebert Alberto; Sala, Evis; Hricak, Hedvig [Memorial Sloan Kettering Cancer Center, Department of Radiology, New York, NY (United States); Grimm, Jan [Memorial Sloan Kettering Cancer Center, Department of Radiology, New York, NY (United States); Program in Molecular Pharmacology and Chemistry, Memorial Sloan Kettering Cancer Center, New York (United States); Donati, Olivio F. [Memorial Sloan Kettering Cancer Center, Department of Radiology, New York, NY (United States); University Hospital Zurich, Institute of Diagnostic and Interventional Radiology, Zurich (Switzerland)

    2015-05-01

    The epidemiology of prostate cancer has dramatically changed since the introduction of prostate-specific antigen (PSA) screening in the 1980's. Most prostate cancers today are detected at early stages of the disease and are considered 'indolent'; however, some patients' prostate cancers demonstrate a more aggressive behaviour which leads to rapid progression and death. Increasing understanding of the biology underlying the heterogeneity that characterises this disease has led to a continuously evolving role of imaging in the management of prostate cancer. Functional and metabolic imaging techniques are gaining importance as the impact on the therapeutic paradigm has shifted from structural tumour detection alone to distinguishing patients with indolent tumours that can be managed conservatively (e.g., by active surveillance) from patients with more aggressive tumours that may require definitive treatment with surgery or radiation. In this review, we discuss advanced imaging techniques that allow direct visualisation of molecular interactions relevant to prostate cancer and their potential for translation to the clinical setting in the near future. The potential use of imaging to follow molecular events during drug therapy as well as the use of imaging agents for therapeutic purposes will also be discussed. (orig.)

  13. Imaging corn plants with PhytoPET, a modular PET system for plant biology

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S.; Kross, B.; McKisson, J.; McKisson, J. E.; Weisenberger, A. G.; Xi, W.; Zorn, C.; Bonito, G.; Howell, C. R.; Reid, C. D.; Crowell, A.; Cumberbatch, L. C.; Topp, C.; Smith, M. F.

    2013-11-01

    PhytoPET is a modular positron emission tomography (PET) system designed specifically for plant imaging. The PhytoPET design allows flexible arrangements of PET detectors based on individual standalone detector modules built from single Hamamatsu H8500 position sensitive photomultiplier tubes and pixelated LYSO arrays. We have used the PhytoPET system to perform preliminary corn plant imaging studies at the Duke University Biology Department Phytotron. Initial evaluation of the PhytoPET system to image the biodistribution of the positron emitting tracer {sup 11}C in corn plants is presented. {sup 11}CO{sub 2} is loaded into corn seedlings by a leaf-labeling cuvette and translocation of {sup 11}C-sugars is imaged by a flexible arrangement of PhytoPET modules on each side. The PhytoPET system successfully images {sup 11}C within corn plants and allows for the dynamic measurement of {sup 11}C-sugar translocation from the leaf to the roots.

  14. Breaching Biological Barriers: Protein Translocation Domains as Tools for Molecular Imaging and Therapy

    Directory of Open Access Journals (Sweden)

    Benjamin L. Franc

    2003-10-01

    Full Text Available The lipid bilayer of a cell presents a significant barrier for the delivery of many molecular imaging reagents into cells at target sites in the body. Protein translocation domains (PTDs are peptides that breach this barrier. Conjugation of PTDs to imaging agents can be utilized to facilitate the delivery of these agents through the cell wall, and in some cases, into the cell nucleus, and have potential for in vitro and in vivo applications. PTD imaging conjugates have included small molecules, peptides, proteins, DNA, metal chelates, and magnetic nanoparticles. The full potential of the use of PTDs in novel in vivo molecular probes is currently under investigation. Cells have been labeled in culture using magnetic nanoparticles derivatized with a PTD and monitored in vivo to assess trafficking patterns relative to cells expressing a target antigen. In vivo imaging of PTD-mediated gene transfer to cells of the skin has been demonstrated in living animals. Here we review several natural and synthetic PTDs that have evolved in the quest for easier translocation across biological barriers and the application of these peptide domains to in vivo delivery of imaging agents.

  15. Understanding God images and God concepts : Towards a pastoral hermeneutics of the God attachment experience

    NARCIS (Netherlands)

    Counted, Agina Victor

    2015-01-01

    The author looks at the God image experience as an attachment relationship experience with God. Hence, arguing that the God image experience is borne originally out of a parent–child attachment contagion, in such a way that God is often represented in either secure or insecure attachment patterns.

  16. Understanding God images and God concepts : Towards a pastoral hermeneutics of the God attachment experience

    NARCIS (Netherlands)

    Counted, Agina Victor

    2015-01-01

    The author looks at the God image experience as an attachment relationship experience with God. Hence, arguing that the God image experience is borne originally out of a parent–child attachment contagion, in such a way that God is often represented in either secure or insecure attachment patterns. T

  17. Molecular Origin of Color Variation in Firefly (Beetle) Bioluminescence: A Chemical Basis for Biological Imaging.

    Science.gov (United States)

    Hirano, Takashi

    2016-01-01

    Firefly shows bioluminescence by "luciferin-luciferase" (L-L) reaction using luciferin, luciferase, ATP and O2. The chemical photon generation by an enzymatic reaction is widely utilized for analytical methods including biological imaging in the life science fields. To expand photondetecting analyses with firefly bioluminescence, it is important for users to understand the chemical basis of the L-L reaction. In particular, the emission color variation of the L-L reaction is one of the distinguishing characteristics for multicolor luciferase assay and in vivo imaging. From the viewpoint of fundamental chemistry, this review explains the recent progress in the studies on the molecular mechanism of emission color variation after showing the outline of the reaction mechanism of the whole L-L reaction. On the basis of the mechanism, the progresses in organic synthesis of luciferin analogs modulating their emission colors are also presented to support further developments of red/near infrared in vivo biological imaging utility of firefly bioluminescence.

  18. Molecular PET imaging for biology-guided adaptive radiotherapy of head and neck cancer

    Energy Technology Data Exchange (ETDEWEB)

    Hoeben, Bianca A. W.; Bussink, Johan; Kaanders, Johannes H. A. M. [Dept. of Radiation Oncology, Radboud Univ. Nijmegen Medical Centre, Nijmegen (Netherlands)], e-mail: b.hoeben@rther.umcn.nl; Oyen, Wim J. G. [Dept. of Nuclear Medicine, Radboud Univ. Nijmegen Medical Centre, Nijmegen (Netherlands); Troost, Esther G. C. [Maastro Clinic, GROW School for Oncology and Developmental Biology, Maastricht Univ. Medical Centre, Maastricht (Netherlands)

    2013-10-15

    Integration of molecular imaging PET techniques into therapy selection strategies and radiation treatment planning for head and neck squamous cell carcinoma (HNSCC) can serve several purposes. First, pre-treatment assessments can steer decisions about radiotherapy modifications or combinations with other modalities. Second, biology-based objective functions can be introduced to the radiation treatment planning process by co-registration of molecular imaging with planning computed tomography (CT) scans. Thus, customized heterogeneous dose distributions can be generated with escalated doses to tumor areas where radiotherapy resistance mechanisms are most prevalent. Third, monitoring of temporal and spatial variations in these radiotherapy resistance mechanisms early during the course of treatment can discriminate responders from non-responders. With such information available shortly after the start of treatment, modifications can be implemented or the radiation treatment plan can be adapted tailing the biological response pattern. Currently, these strategies are in various phases of clinical testing, mostly in single-center studies. Further validation in multicenter set-up is needed. Ultimately, this should result in availability for routine clinical practice requiring stable production and accessibility of tracers, reproducibility and standardization of imaging and analysis methods, as well as general availability of knowledge and expertise. Small studies employing adaptive radiotherapy based on functional dynamics and early response mechanisms demonstrate promising results. In this context, we focus this review on the widely used PET tracer 18F-FDG and PET tracers depicting hypoxia and proliferation; two well-known radiation resistance mechanisms.

  19. Shortwave-infrared (SWIR emitters for biological imaging: a review of challenges and opportunities

    Directory of Open Access Journals (Sweden)

    Thimsen Elijah

    2017-08-01

    Full Text Available Shortwave infrared radiation (SWIR is the portion of the electromagnetic spectrum from approximately 900 nm to 2500 nm. Recent advances in imaging systems have expanded the application of SWIR emitters from traditional fields in materials science to biomedical imaging, and the new detectors in SWIR opened an opportunity of deep tissue imaging. Achieving deep photon penetration while maintaining high resolution is one of the main objectives and challenges in bioimaging used for the investigation of diverse processes in living organisms. The application of SWIR emitters in biological settings is, however, hampered by low quantum efficiency. So far, photoluminescent properties in the SWIR region have not been improved by extending concepts that have been developed for the visible (400–650 nm and near-infrared (NIR, 700–900 nm wavelengths, which indicates that the governing behavior is fundamentally different in the SWIR. The focus of this minireview is to examine the mechanisms behind the low efficiency of SWIR emitters as well as to highlight the progress in their design for biological applications. Several common mechanisms will be considered in this review: (a the effect of the energy gap between the excited and ground state on the quantum efficiency, (b the coupling of the excited electronic states in SWIR emitters to vibrational states in the surrounding matrix, and (c the role of environment in quenching the excited states. General strategies to improve the quantum yields for a diverse type of SWIR emitters will be also presented.

  20. Molecular PET imaging for biology-guided adaptive radiotherapy of head and neck cancer.

    Science.gov (United States)

    Hoeben, Bianca A W; Bussink, Johan; Troost, Esther G C; Oyen, Wim J G; Kaanders, Johannes H A M

    2013-10-01

    Integration of molecular imaging PET techniques into therapy selection strategies and radiation treatment planning for head and neck squamous cell carcinoma (HNSCC) can serve several purposes. First, pre-treatment assessments can steer decisions about radiotherapy modifications or combinations with other modalities. Second, biology-based objective functions can be introduced to the radiation treatment planning process by co-registration of molecular imaging with planning computed tomography (CT) scans. Thus, customized heterogeneous dose distributions can be generated with escalated doses to tumor areas where radiotherapy resistance mechanisms are most prevalent. Third, monitoring of temporal and spatial variations in these radiotherapy resistance mechanisms early during the course of treatment can discriminate responders from non-responders. With such information available shortly after the start of treatment, modifications can be implemented or the radiation treatment plan can be adapted tailing the biological response pattern. Currently, these strategies are in various phases of clinical testing, mostly in single-center studies. Further validation in multicenter set-up is needed. Ultimately, this should result in availability for routine clinical practice requiring stable production and accessibility of tracers, reproducibility and standardization of imaging and analysis methods, as well as general availability of knowledge and expertise. Small studies employing adaptive radiotherapy based on functional dynamics and early response mechanisms demonstrate promising results. In this context, we focus this review on the widely used PET tracer (18)F-FDG and PET tracers depicting hypoxia and proliferation; two well-known radiation resistance mechanisms.

  1. Reflection Imaging X-Ray Laser Microscope (RIXRALM) and its biological applications. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Suckewer, S.

    1998-07-01

    The main stimulus for the development of the proposed microscope (RIXRALM) is the possibility to view the surface and near surface structure of biological materials, such as cell membranes at much higher resolution than an optical (confocal) microscope. Although the prediction resolution of RIXRALM was lower than a Scanning Electron Microscope (SEM), the possibility to obtain images of cells (membranes) in a more natural, hydrated state and, in many cases, without staining, made the idea of a reflection X-ray microscope very attractive. The specimen can be in an H{sub 2}O saturated He atmosphere at atmospheric pressure. As the image can be obtained quickly (nsec exposure, occurring within seconds of insertion into such an environment), the cell surface can be seen in a state which is very close to its natural condition. Besides, the short exposure time eliminates the effect of motional blurring on the images. Their X-ray reflection microscope fit well in the very large gap in the size of biological objects studied in light microscopy (sub-micron size) and electron microscope (down to a few nanometers size).

  2. Shortwave-infrared (SWIR) emitters for biological imaging: a review of challenges and opportunities

    Science.gov (United States)

    Thimsen, Elijah; Sadtler, Bryce; Berezin, Mikhail Y.

    2017-06-01

    Shortwave infrared radiation (SWIR) is the portion of the electromagnetic spectrum from approximately 900 nm to 2500 nm. Recent advances in imaging systems have expanded the application of SWIR emitters from traditional fields in materials science to biomedical imaging, and the new detectors in SWIR opened an opportunity of deep tissue imaging. Achieving deep photon penetration while maintaining high resolution is one of the main objectives and challenges in bioimaging used for the investigation of diverse processes in living organisms. The application of SWIR emitters in biological settings is, however, hampered by low quantum efficiency. So far, photoluminescent properties in the SWIR region have not been improved by extending concepts that have been developed for the visible (400-650 nm) and near-infrared (NIR, 700-900 nm) wavelengths, which indicates that the governing behavior is fundamentally different in the SWIR. The focus of this minireview is to examine the mechanisms behind the low efficiency of SWIR emitters as well as to highlight the progress in their design for biological applications. Several common mechanisms will be considered in this review: (a) the effect of the energy gap between the excited and ground state on the quantum efficiency, (b) the coupling of the excited electronic states in SWIR emitters to vibrational states in the surrounding matrix, and (c) the role of environment in quenching the excited states. General strategies to improve the quantum yields for a diverse type of SWIR emitters will be also presented.

  3. Carbon loaded Teflon (CLT): a power density meter for biological experiments using millimeter waves.

    Science.gov (United States)

    Allen, Stewart J; Ross, James A

    2007-01-01

    The standard technique for measurement of millimeter wave fields utilizes an open-ended waveguide attached to a HP power meter. The alignment of the waveguide with the propagation (K) vector is critical to making accurate measurements. Using this technique, it is difficult and time consuming to make a detailed map of average incident power density over areas of biological interest and the spatial resolution of this instrument does not allow accurate measurements in non-uniform fields. For biological experiments, it is important to know the center field average incident power density and the distribution over the exposed area. Two 4 ft x 4 ft x 1/32 inch sheets of carbon loaded Teflon (CLT) (one 15% carbon and one 25% carbon) were procured and a series of tests to determine the usefulness of CLT in defining fields in the millimeter wavelength range was initiated. Since the CLT was to be used both in the laboratory, where the environment was well controlled, and in the field, where the environment could not be controlled, tests were made to determine effects of change in environmental conditions on ability to use CLT as a millimeter wave dosimeter. The empirical results of this study indicate CLT to be an effective dosimeter for biological experiments both in the laboratory and in the field.

  4. Numerical simulation and experiment of optothermal response of biological tissue irradiated by continuous xenon lamp

    Institute of Scientific and Technical Information of China (English)

    Meizhen Huang; Yaxing Tong

    2012-01-01

    A finite element method computation model for analyzing optothermal interaction of polychromatic light and biology tissue is proposed and proven by experiment.A continuous xenon lamp is employed as an example.First,the spectral energy distribution of the xenon lamp is measured and found to be equivalent to a series of quasi-chromatic light with different central wavelengths,different energies,and certain bandwidth.Next,according to the reported thermal and optical parameters of porcine skin and porcine liver,the temporal temperature distributions of these tissues irradiated by each quasi-chromatic light are simulated.Then,the thermal effect is superimposed to obtain the whole optothermal temporal temperature distribution.Moreover,the optothermal response experiments of fresh porcine skin and porcine liver tissues irradiated by continuous xenon lamp are carried out.The results of the simulation and experiment are analyzed and compared,and are found to be commendably matched.

  5. Psychological and Biological Validation of a Novel Digital Social Peer Evaluation Experiment (digi-SPEE).

    Science.gov (United States)

    Menne-Lothmann, Claudia; Decoster, Jeroen; van Winkel, Ruud; Collip, Dina; Rutten, Bart P F; Delespaul, Philippe; De Hert, Marc; Derom, Catherine; Thiery, Evert; Jacobs, Nele; van Os, Jim; Wichers, Marieke

    2017-03-01

    Negative social evaluation is associated with psychopathology. Given the frequency of evaluation through increasingly prevalent virtual social networks, increased understanding of the effects of this social evaluation is urgently required. A new digital social peer evaluation experiment (digi-SPEE) was developed to mimic everyday online social interactions between peers. Participants received mildly negative feedback on their appearance, intelligence, and congeniality. Two hundred and forty-one young people [58.9% female, aged 18.9 years (15 to 34)] from an ongoing novel general population twin study participated in this study. Positive affect (PA), negative affect (NA), implicit self-esteem, and cortisol were assessed before and after exposure to the social evaluation experiment. The social evaluation experiment decreased PA (B=-5.25, pdigi-SPEE represents a social evaluation stressor that elicits biological and implicit and explicit mental changes that are relevant to mechanisms of psychopathology.

  6. Greenhouse Gas Laser Imaging Tomography Experiment (GreenLITE

    Directory of Open Access Journals (Sweden)

    Dobler Jeremy

    2016-01-01

    Full Text Available Exelis has recently developed a novel laser-based instrument to aid in the autonomous real-time monitoring and mapping of CO2 concentration over a two-dimensional area. The Greenhouse gas Laser Imaging Tomography Experiment (GreenLITE instrument uses two transceivers and a series of retroreflectors to continuously measure the differential transmission over a number of overlapping lines of sight or “chords”, forming a plane. By inverting the differential transmission measurements along with locally measured temperature (T, pressure (P and relative humidity (RH the average concentration of CO2 along each chord can be determined and, based on the overlap between chords, a 2D map of CO2 concentration over the measurement plane can be estimated. The GreenLITE system was deployed to the Zero Emissions Research and Technology (ZERT center in Bozeman, Montana, in Aug-Sept 2014, where more than 200 hours of data were collected over a wide range of environmental conditions, while utilizing a controlled release of CO2 into a segmented underground pipe [1]. The system demonstrated the ability to identify persistent CO2 sources at the test facility and showed strong correlation with an independent measurement using a LI-COR based system. Here we describe the measurement approach, instrument design, and results from the deployment to the ZERT site.

  7. Non-Chemical Distant Cellular Interactions as a potential confounder of cell biology experiments.

    Science.gov (United States)

    Farhadi, Ashkan

    2014-01-01

    Distant cells can communicate with each other through a variety of methods. Two such methods involve electrical and/or chemical mechanisms. Non-chemical, distant cellular interactions may be another method of communication that cells can use to modify the behavior of other cells that are mechanically separated. Moreover, non-chemical, distant cellular interactions may explain some cases of confounding effects in Cell Biology experiments. In this article, we review non-chemical, distant cellular interactions studies to try to shed light on the mechanisms in this highly unconventional field of cell biology. Despite the existence of several theories that try to explain the mechanism of non-chemical, distant cellular interactions, this phenomenon is still speculative. Among candidate mechanisms, electromagnetic waves appear to have the most experimental support. In this brief article, we try to answer a few key questions that may further clarify this mechanism.

  8. Non-Chemical Distant Cellular Interactions as a potential confounder of Cell Biology Experiments

    Directory of Open Access Journals (Sweden)

    Ashkan eFarhadi

    2014-10-01

    Full Text Available Distant cells can communicate with each other through a variety of methods. Two such methods involve electrical and/or chemical mechanisms. Non-chemical, distant cellular interactions may be another method of communication that cells can use to modify the behavior of other cells that are mechanically separated. Moreover, non-chemical, distant cellular interactions may explain some cases of confounding effects in Cell Biology experiments. In this article, we review non-chemical, distant cellular interactions studies to try to shed light on the mechanisms in this highly unconventional field of cell biology. Despite the existence of several theories that try to explain the mechanism of non-chemical, distant cellular interactions, this phenomenon is still speculative. Among candidate mechanisms, electromagnetic waves appear to have the most experimental support. In this brief article, we try to answer a few key questions that may further clarify this mechanism.

  9. Reproducibility of High-Throughput Plate-Reader Experiments in Synthetic Biology.

    Science.gov (United States)

    Chavez, Michael; Ho, Jonathan; Tan, Cheemeng

    2017-02-17

    Plate-reader assays are commonly conducted to quantify the performance of synthetic biological systems. However, on the basis of a survey of 100 publications, we find that most publications do not report critical experimental settings of plate reader assays, suggesting widespread issues in their reproducibility. Specifically, critical plate reader settings, including shaking time and covering method, either vary between laboratories or are not reported by the publications. Here, we demonstrate that the settings of plate reader assays have a significant impact on bacterial growth, recombinant gene expression, and biofilm formation. Furthermore, we show that the plate reader settings affect the apparent activity, sensitivity, and chemical kinetics of synthetic constructs, as well as alter the apparent effectiveness of antibiotics. Our results suggest the critical need for consistent reporting of plate reader protocols to ensure the reproducibility of the protocols. In addition, our work provides data for the setup of plate reader protocols in synthetic biology experiments.

  10. Non-destructive high-resolution thermal imaging techniques to evaluate wildlife and delicate biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Lavers, C; Franklin, P; Franklin, P; Plowman, A; Sayers, G; Bol, J; Shepard, D; Fields, D, E-mail: brnc-radarcomms1@nrta.mod.u [Sensors Team, Plymouth University at Britannia Royal Naval College, Dartmouth, Devon (United Kingdom) and Paignton Zoological Park, Paignton, Devon (United Kingdom); Thermal Wave Imaging, Inc., 845 Livernoise St, Ferndale, MI (United States); Buckfast Butterfly and Otter Sanctuary, Buckfast, Devon (United Kingdom)

    2009-07-01

    Thermal imaging cameras now allows routine monitoring of dangerous yet endangered wildlife in captivity. This study looks at the potential applications of radiometrically calibrated thermal data to wildlife, as well as providing parameters for future materials applications. We present a non-destructive active testing technique suitable for enhancing imagery contrast of thin or delicate biological specimens yielding improved thermal contrast at room temperature, for analysis of sample thermal properties. A broad spectrum of animals is studied with different textured surfaces, reflective and emissive properties in the infra red part of the electromagnetic spectrum. Some surface features offer biomimetic materials design opportunities.

  11. Recent development of biotin conjugation in biological imaging, sensing, and target delivery.

    Science.gov (United States)

    Ren, Wen Xiu; Han, Jiyou; Uhm, Soojin; Jang, Yu Jin; Kang, Chulhun; Kim, Jong-Hoon; Kim, Jong Seung

    2015-07-04

    Despite encouraging results from preliminary studies of anticancer therapies, the lack of tumor specificity remains an important issue in the modern pharmaceutical industry. New findings indicate that biotin or biotin-conjugates could be favorably assimilated by tumor cells that over-express biotin-selective transporters. Furthermore, biotin can form stable complexes with avidin and its bacterial counterpart streptavidin. The strong bridging between avidin and biotin moieties on other molecules is a proven adaptable tool with broad biological applications. Under these circumstances, a biotin moiety is certainly an attractive choice for live-cell imaging, biosensing, and target delivery.

  12. Phase Sensitive X-Ray Diffraction Imaging of Defects in Biological Macromolecular Crystals

    Science.gov (United States)

    Hu, Z. W.; Lai, B.; Chu, Y. S.; Cai, Z.; Mancini, D. C.; Thomas, B. R.; Chernov, A. A.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    Characterization of defects and/or disorder in biological macromolecular crystals presents much greater challenges than in conventional small-molecule crystals. The lack of sufficient contrast of defects is often a limiting factor in x-ray diffraction topography of protein crystals. This has seriously hampered efforts to understand mechanisms and origins of formation of imperfections, and the role of defects as essential entities in the bulk of macromolecular crystals. In this report, we employ a phase sensitive x-ray diffraction imaging approach for augmenting the contrast of defects in protein crystals.

  13. Micro-computed tomography imaging and analysis in developmental biology and toxicology.

    Science.gov (United States)

    Wise, L David; Winkelmann, Christopher T; Dogdas, Belma; Bagchi, Ansuman

    2013-06-01

    Micro-computed tomography (micro-CT) is a high resolution imaging technique that has expanded and strengthened in use since it was last reviewed in this journal in 2004. The technology has expanded to include more detailed analysis of bone, as well as soft tissues, by use of various contrast agents. It is increasingly applied to questions in developmental biology and developmental toxicology. Relatively high-throughput protocols now provide a powerful and efficient means to evaluate embryos and fetuses subjected to genetic manipulations or chemical exposures. This review provides an overview of the technology, including scanning, reconstruction, visualization, segmentation, and analysis of micro-CT generated images. This is followed by a review of more recent applications of the technology in some common laboratory species that highlight the diverse issues that can be addressed.

  14. PET and SPECT Imaging of Tumor Biology: New Approaches towards Oncology Drug Discovery and Development.

    Science.gov (United States)

    Van Dort, Marcian E; Rehemtulla, Alnawaz; Ross, Brian D

    2008-01-01

    Spiraling drug developmental costs and lengthy time-to-market introduction are two critical challenges facing the pharmaceutical industry. The clinical trials success rate for oncology drugs is reported to be 5% as compared to other therapeutic categories (11%) with most failures often encountered late in the clinical development process. PET and SPECT nuclear imaging technologies could play an important role in facilitating the drug development process improving the speed, efficiency and cost of drug development. This review will focus on recent studies of PET and SPECT radioligands in oncology and their application in the investigation of tumor biology. The use of clinically-validated radioligands as imaging-based biomarkers in oncology could significantly impact new cancer therapeutic development.

  15. Prediction of intracellular storage polymers using quantitative image analysis in enhanced biological phosphorus removal systems.

    Science.gov (United States)

    Mesquita, Daniela P; Leal, Cristiano; Cunha, Jorge R; Oehmen, Adrian; Amaral, A Luís; Reis, Maria A M; Ferreira, Eugénio C

    2013-04-03

    The present study focuses on predicting the concentration of intracellular storage polymers in enhanced biological phosphorus removal (EBPR) systems. For that purpose, quantitative image analysis techniques were developed for determining the intracellular concentrations of PHA (PHB and PHV) with Nile blue and glycogen with aniline blue staining. Partial least squares (PLS) were used to predict the standard analytical values of these polymers by the proposed methodology. Identification of the aerobic and anaerobic stages proved to be crucial for improving the assessment of PHA, PHB and PHV intracellular concentrations. Current Nile blue based methodology can be seen as a feasible starting point for further enhancement. Glycogen detection based on the developed aniline blue staining methodology combined with the image analysis data proved to be a promising technique, toward the elimination of the need for analytical off-line measurements. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, Subhash [Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Snee Hall, Cornell University, Ithaca, NY 14853 (United States)], E-mail: sc40@cornell.edu

    2008-12-15

    Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O{sub 2}{sup +}) revealed local secondary ion signal enhancements correlated with the water image signals of {sup 19}(H{sub 3}O){sup +}. A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K{sup +} and Na{sup +} in physiologically relevant concentrations. The high K

  17. Main results of biological experiments on Russian orbital stations and its contribution in future life support system

    Science.gov (United States)

    Nechitailo, Galina S.

    Biological experiments in a field of space biology have been started before the first satellite flight. These experiments were devoted to an estimation of space radiation factors on living organisms and carried out in mountains. The systematic biological experiments in space have been started in 1971 with orbital station Salyut. In total more than 1000 experiments have been installed in space flights: fundamental investigations (panspermia theory, gravity biology, complex factors of space environment on biological objects) and applications focused on future biological life support systems. The investigations were directed to some tasks: influence of complex factors of space flight on living organisms at different stages of the evolution scale; investigations of proteins and DNA, cell, tissue, organism and assembled organisms under space flight factors with separation of individual factors, for example, microgravity and space radiation. The aim was to understand the organism reactions on different levels, to get complete ontogenesis cycle in space flight and to find adaption ability of organisms to extreme factors of the space flight. In course of investigations, the unique experimental equipment for orbital biological experiments has been designed; new methods for organism protection against the negative factors of space flight were found; developed new biotechnological products and processes; developed recommendations for space station interior with biological objects for psychological comfort of crew. The results showed a possibility and ways to include different organisms into biotechnological life support systems for future space stations and interplanet spaceships.

  18. Analysis of Images from Experiments Investigating Fragmentation of Materials

    Energy Technology Data Exchange (ETDEWEB)

    Kamath, C; Hurricane, O

    2007-09-10

    Image processing techniques have been used extensively to identify objects of interest in image data and extract representative characteristics for these objects. However, this can be a challenge due to the presence of noise in the images and the variation across images in a dataset. When the number of images to be analyzed is large, the algorithms used must also be relatively insensitive to the choice of parameters and lend themselves to partial or full automation. This not only avoids manual analysis which can be time consuming and error-prone, but also makes the analysis reproducible, thus enabling comparisons between images which have been processed in an identical manner. In this paper, we describe our approach to extracting features for objects of interest in experimental images. Focusing on the specific problem of fragmentation of materials, we show how we can extract statistics for the fragments and the gaps between them.

  19. Handheld hyperspectral imager system for chemical/biological and environmental applications

    Science.gov (United States)

    Hinnrichs, Michele; Piatek, Bob

    2004-08-01

    A small, hand held, battery operated imaging infrared spectrometer, Sherlock, has been developed by Pacific Advanced Technology and was field tested in early 2003. The Sherlock spectral imaging camera has been designed for remote gas leak detection, however, the architecture of the camera is versatile enough that it can be applied to numerous other applications such as homeland security, chemical/biological agent detection, medical and pharmaceutical applications as well as standard research and development. This paper describes the Sherlock camera, theory of operations, shows current applications and touches on potential future applications for the camera. The Sherlock has an embedded Power PC and performs real-time-image processing function in an embedded FPGA. The camera has a built in LCD display as well as output to a standard monitor, or NTSC display. It has several I/O ports, ethernet, firewire, RS232 and thus can be easily controlled from a remote location. In addition, software upgrades can be performed over the ethernet eliminating the need to send the camera back to the factory for a retrofit. Using the USB port a mouse and key board can be connected and the camera can be used in a laboratory environment as a stand alone imaging spectrometer.

  20. Biological tissue imaging with a hybrid cluster SIMS quadrupole time-of-flight mass spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Carado, A. [Pennsylvania State University, 104 Chemistry Building, University Park, PA (United States)], E-mail: ajc161@psu.edu; Kozole, J.; Passarelli, M.; Winograd, N. [Pennsylvania State University, 104 Chemistry Building, University Park, PA (United States); Loboda, A. [Applied Biosystems/MDS Sciex, 71 Four Valley Drive, Concord, Ontario, CA (United States); Bunch, J. [Centre for Analytical Sciences, University of Sheffield, Sheffield S3 7HF (United Kingdom); Wingate, J. [Applied Biosystems/MDS Sciex, 71 Four Valley Drive, Concord, Ontario, CA (United States); Hankin, J.; Murphy, R. [University of Colorado at Denver and Health Science Center, 12801 East 17th Avenue, Aurora, CO (United States)

    2008-12-15

    A 20 keV C{sub 60}{sup +} ion source was mounted onto a commercial MALDI/electrospray orthogonal ToF mass spectrometer. Cross-sectional mouse brain and lung slices between 5 and 10 {mu}m prepared by cryostat sectioning were successfully imaged using a DC C{sub 60}{sup +} primary ion beam at a spot size of 100 {mu}m. Analysis was performed at room temperature following vacuum drying. An abundance of ions were mapped in all samples, many whose identity can only be found using the MS/MS functionality. We have successfully identified and imaged localizations of diacylglycerol (DAG) ions - 1-palmitoyl-2-oleoyl-glycerol (m/z{sup +} 577.5) and 1,2-dioleoyl-glycerol (m/z{sup +} 603.5) - in lung tissue. The mouse brain slice revealed strong, distinct localizations of many ions revealing the potential for this technique for biological imaging. Ions throughout the mass range of m/z{sup +} 50-800 were collected in sufficient quantities to permit unambiguous chemical mapping. Mass resolutions of 12,000 or greater were routinely obtained allowing for more accurate ion mapping than typically seen with ToF-SIMS image analysis.

  1. Competition Between Biosimilars and Patented Biologics: Learning from European and Japanese Experience.

    Science.gov (United States)

    Bocquet, François; Loubière, Anaïs; Fusier, Isabelle; Cordonnier, Anne-Laure; Paubel, Pascal

    2016-11-01

    The expiry of patents for costly biologics is creating new momentum on the pharmaceutical market for biosimilars (copies of off-patent biologics) and paving the way for their development. However, little is known about the competitiveness of biosimilars versus their originators and other biologics belonging to the same therapeutic class. The main goal of this study was to analyse the type of competition generated by the first biosimilars commercialised on key global biologic markets and to grasp their economic model. The secondary goal was to distinguish the main factors likely to influence the uptake of biosimilars on national markets. To be included in this study, countries had to meet three conditions: the regulatory framework for the development of biosimilars closely resembled that in Europe, biosimilars were marketed in 2014, and the value of the biologics market was >US$3 billion. We analysed granulocyte colony-stimulating factors (GCSFs) and erythropoietins (EPOs) over the period 2007-2014 because these are the two main therapeutic classes that have been 'biosimilarised' and thus have many years of experience available. We assessed market sizes, retail/hospital distribution mixes, incentives for using biosimilars and price discounts for originators versus biosimilars. We conducted a linear regression analysis to assess the relationship between uptakes of biosimilars and the market shares of other biologics. The EU-5 (France, Germany, Italy, Spain and the UK) and Japanese GCSF and EPO markets are highly-country-specific. Uptake of biosimilars seems to depend on retail/hospital distribution mixes and on medical practice. Depending on the therapeutic class and the market sector (retail or hospital), biosimilars may compete with first-generation or second-generation products or both. Some incentives implemented to encourage the use of biosimilars had mixed results. Overall, discounts for biosimilars versus originators are not factors that determine global

  2. X-ray imaging and imaging spectroscopy of fusion plasmas and light-source experiments with spherical optics and pixel array detectors

    Science.gov (United States)

    Hill, K. W.; Bitter, M.; Delgado-Aparicio, L.; Pablant, N. A.; Beiersdorfer, P.; Sanchez del Rio, M.; Zhang, L.

    2012-10-01

    High resolution (λ/Δλ ~10,000) 1D imaging x-ray spectroscopy using a spherically bent crystal and a 2D hybrid pixelarray detector (PAD) is used world wide for Doppler measurements of ion-temperature (Ti) and plasma flow-velocityprofiles in magnetic confinement fusion (MCF) plasmas. Meter sized plasmas are diagnosed with cm spatial resolution and 10 ms time resolution. This concept can also be used as a diagnostic of small sources, such as inertial confinement fusion (ICF) plasmas and targets on x-ray light source beam lines, with spatial resolution of microns. A new concept of using matched pairs of spherically bent crystals for monochromatic stigmatic 2D x-ray imaging of mm sized sources offers the possibility of spatial resolution of microns and large solid angle, relative to that achieved with pinhole imaging. Other potential applications of the 2D imaging schemes include x-ray lithography and x-ray microscopy for biological and materials science research. Measurements from MFE plasmas, as well as laboratory experiments and ray tracing computations validating the 1D imaging spectroscopy and 2D x-ray imaging techniques will be presented.

  3. Iron and mixing affect biological carbon uptake in SOIREE and EisenEx, two Southern Ocean iron fertilisation experiments

    NARCIS (Netherlands)

    Bakker, Dorothee C.E.; Bozec, Yann; Nightingale, Philip D.; Goldson, Laura; Messias, Marie-José; Baar, Hein J.W. de; Liddicoat, Malcolm; Skjelvan, Ingunn; Strass, Volker; Watson, Andrew J.

    2005-01-01

    This study explores the changes in the surface water fugacity of carbon dioxide (fCO2) and biological carbon uptake in two Southern Ocean iron fertilisation experiments with different hydrographic regimes. The Southern Ocean Iron Release Experiment (SOIREE) experiment was carried out south of the An

  4. Extending Whole Slide Imaging: Color Darkfield Internal Reflection Illumination (DIRI) for Biological Applications

    Science.gov (United States)

    Namiki, Kana; Miyawaki, Atsushi; Ishikawa, Takuji

    2017-01-01

    Whole slide imaging (WSI) is a useful tool for multi-modal imaging, and in our work, we have often combined WSI with darkfield microscopy. However, traditional darkfield microscopy cannot use a single condenser to support high- and low-numerical-aperture objectives, which limits the modality of WSI. To overcome this limitation, we previously developed a darkfield internal reflection illumination (DIRI) microscope using white light-emitting diodes (LEDs). Although the developed DIRI is useful for biological applications, substantial problems remain to be resolved. In this study, we propose a novel illumination technique called color DIRI. The use of three-color LEDs dramatically improves the capability of the system, such that color DIRI (1) enables optimization of the illumination color; (2) can be combined with an oil objective lens; (3) can produce fluorescence excitation illumination; (4) can adjust the wavelength of light to avoid cell damage or reactions; and (5) can be used as a photostimulator. These results clearly illustrate that the proposed color DIRI can significantly extend WSI modalities for biological applications. PMID:28085892

  5. Photoacoustic Imaging in Oncology: Translational Preclinical and Early Clinical Experience.

    Science.gov (United States)

    Valluru, Keerthi S; Wilson, Katheryne E; Willmann, Jürgen K

    2016-08-01

    Photoacoustic imaging has evolved into a clinically translatable platform with the potential to complement existing imaging techniques for the management of cancer, including detection, characterization, prognosis, and treatment monitoring. In photoacoustic imaging, tissue is optically excited to produce ultrasonographic images that represent a spatial map of optical absorption of endogenous constituents such as hemoglobin, fat, melanin, and water or exogenous contrast agents such as dyes and nanoparticles. It can therefore provide functional and molecular information that allows noninvasive soft-tissue characterization. Photoacoustic imaging has matured over the years and is currently being translated into the clinic with various clinical studies underway. In this review, the current state of photoacoustic imaging is presented, including techniques and instrumentation, followed by a discussion of potential clinical applications of this technique for the detection and management of cancer. (©) RSNA, 2016.

  6. Teaching Fluid Mechanics for Undergraduate Students in Applied Industrial Biology: from Theory to Atypical Experiments

    CERN Document Server

    Absi, Rafik; Dufour, Florence; Huet, Denis; Bennacer, Rachid; Absi, Tahar

    2011-01-01

    EBI is a further education establishment which provides education in applied industrial biology at level of MSc engineering degree. Fluid mechanics at EBI was considered by students as difficult who seemed somewhat unmotivated. In order to motivate them, we applied a new play-based pedagogy. Students were asked to draw inspiration from everyday life situations to find applications of fluid mechanics and to do experiments to verify and validate some theoretical results obtained in course. In this paper, we present an innovative teaching/learning pedagogy which includes the concept of learning through play and its implications in fluid mechanics for engineering. Examples of atypical experiments in fluid mechanics made by students are presented. Based on teaching evaluation by students, it is possible to know how students feel the course. The effectiveness of this approach to motivate students is presented through an analysis of students' teaching assessment. Learning through play proved a great success in fluid...

  7. An exploration of student experiences of using biology podcasts in nursing training

    Directory of Open Access Journals (Sweden)

    Mostyn Alison

    2013-01-01

    Full Text Available Abstract Background Students regard biological science as one of the most difficult components of the nursing curriculum. However, a good understanding of this area is essential for effective nursing practice. The aim of this study was to explore nursing students’ perceptions of the usefulness of supplementary biology podcasts for their learning. Methods Biological science podcasts (n = 9 were made available to first-year nursing students (n = 189 as supplementary learning tools. On completion of their first year, students were asked to complete a survey which investigated the frequency of their podcast use, reasons for use and their perception of the usefulness of podcasts as a learning tool. 153 of these students participated in the survey study (80.9%. Two focus groups were conducted with students (n = 6 to gain a detailed understanding of student experiences of the usefulness of the podcasts for their learning. Results Survey data demonstrated that most students (71% accessed at least one podcast. The majority of students who reported accessing podcasts agreed that they were useful as learning tools (83%, revision aids (83% and that they helped promote understanding of course materials (72%. Focus group participants discussed how they found podcasts especially useful in terms of revision. Students valued being able to repeatedly access the lecture materials, and appreciated having access to podcasts from a range of lecturers. Focus group members discussed the benefits of live recordings, in terms of valuing the information gleaned from questions asked during the lecture sessions, although there were concerns about the level of background noise in live recordings. Lack of awareness of the availability of podcasts was an issue raised by participants in both the survey component and the focus groups and this negatively impacted on podcast use. Conclusions Nursing students found the availability of biology podcasts helpful for

  8. Ten Years’ Experience with an E-Learning Lecture Series on Cancer Biology and Pharmacology

    Directory of Open Access Journals (Sweden)

    Thomas Efferth

    2013-01-01

    Full Text Available In life sciences, the internet is an indispensable medium for research, but has not yet realized its full potential for teaching. The concept of e-learning has been developed over the past decades for undergraduate, graduate and postgraduate programs. We set up an e-learning lecture on cancer biology and pharmacology that was first offered in 2003 to students of Molecular Biotechnology at the University of Heidelberg and to students of Pharmacy at the University of Mainz, Germany. The present paper recapitulates the first decade of experiences with this e-learning lecture from both the students’ and the teachers’ perspectives. A total of 317 students during the past 10 years participated in a survey. In general, the students enjoyed the possibilities that self-controlled learning offers. E-learning interested them as a novel educational method. They felt quite comfortable listening to the material despite the interdisciplinary nature of the lectures, which included molecular biological, pharmacological and medical aspects of cancer biology and pharmacology. This lecture was the first e-learning experience for the majority of students, and their impressions were generally positive. The students not only indicated that they would like to continue with e-learning, but also would recommend e-learning to other students. Remarkably, the majority of students would like to see more e-learning offered in their present curricula. They indicated interest in mixed forms of traditional learning and e-learning (“blended learning”, although it is recognized that face-to-face contact between teachers and students is critical. Overall, many students would consider e-learning for further and continuing education after graduation.

  9. Understanding God images and God concepts: Towards a pastoral hermeneutics of the God attachment experience

    Directory of Open Access Journals (Sweden)

    Victor Counted

    2015-03-01

    Full Text Available The author looks at the God image experience as an attachment relationship experience with God. Hence, arguing that the God image experience is borne originally out of a parent�child attachment contagion, in such a way that God is often represented in either secure or insecure attachment patterns. The article points out that insecure God images often develop head-to-head with God concepts in a believer�s emotional experience of God. On the other hand, the author describes God concepts as indicators of a religious faith and metaphorical standards for regulating insecure attachment patterns. The goals of this article, however, is to highlight the relationship between God images and God concepts, and to provide a hermeneutical process for interpreting and surviving the God image experience.Intradisciplinary and/or interdisciplinary implications: Given that most scholars within the discipline of Practical Theology discuss the subject of God images from cultural and theological perspectives, this article has discussed God images from an attachment perspective, which is a popular framework in psychology of religion. This is rare. The study is therefore interdisciplinary in this regards. The article further helps the reader to understand the intrapsychic process of the God image experience, and thus provides us with hermeneutical answers for dealing with the God image experience from methodologies grounded in Practical Theology and pastoral care.

  10. Destroying False Images of God: The Experiences of LGBT Catholics.

    Science.gov (United States)

    Deguara, Angele

    2017-04-10

    This article is about how lesbian, gay, bisexual, and trans (LGBT) Catholics imagine God and how images of God change in parallel with their self-image. The study is based on qualitative research with LGBT Catholics, most of whom are members of Drachma LGBTI in Malta or Ali d'Aquila in Palermo, Sicily. LGBT Catholics' image of God changes as they struggle to reconcile their religious and sexual identities and as they go through a process of "conversion" from deviants and sinners to loved children of God. One study participant compares his faith in God to peeling an onion: "With every layer one peels off, one destroys false images of God." Most study participants have moved away from the image of God as a bearded old man and father of creation and moved more toward a conception of God as love once identity conflicts are resolved.

  11. A photoelastic modulator-based birefringence imaging microscope for measuring biological specimens

    Science.gov (United States)

    Freudenthal, John; Leadbetter, Andy; Wolf, Jacob; Wang, Baoliang; Segal, Solomon

    2014-11-01

    The photoelastic modulator (PEM) has been applied to a variety of polarimetric measurements. However, nearly all such applications use point-measurements where each point (spot) on the sample is measured one at a time. The main challenge for employing the PEM in a camera-based imaging instrument is that the PEM modulates too fast for typical cameras. The PEM modulates at tens of KHz. To capture the specific polarization information that is carried on the modulation frequency of the PEM, the camera needs to be at least ten times faster. However, the typical frame rates of common cameras are only in the tens or hundreds frames per second. In this paper, we report a PEM-camera birefringence imaging microscope. We use the so-called stroboscopic illumination method to overcome the incompatibility of the high frequency of the PEM to the relatively slow frame rate of a camera. We trigger the LED light source using a field-programmable gate array (FPGA) in synchrony with the modulation of the PEM. We show the measurement results of several standard birefringent samples as a part of the instrument calibration. Furthermore, we show results observed in two birefringent biological specimens, a human skin tissue that contains collagen and a slice of mouse brain that contains bundles of myelinated axonal fibers. Novel applications of this PEM-based birefringence imaging microscope to both research communities and industrial applications are being tested.

  12. Edge-Preserving Regularization for the Deconvolution of Biological Images in Nanoscopy

    Science.gov (United States)

    Sawatzky, Alex; Burger, Martin

    2010-09-01

    This paper deals with reconstructions of density images from data with Poisson statistics, with particular focus on cartoon reconstructions. We propose a total variation (TV) based regularization technique adapted to the case of Poisson data and use a forward-backward (FB) splitting strategy to create a numerical scheme that alternates a standard Expectation-Maximization (EM) reconstruction step with a TV correction step, which is realized by a modified version of the Rudin-Osher-Fatemi (ROF) model. We illustrate our technique at a synthetic object simulating optical nanoscopy measurements. Inspired by the high redundancy of information in a typical biological image, we give an outlook for an extension of the FB-EM-TV method to a nonlocal TV (NL-TV) regularization. NL-TV uses a nonlocal graph regularization, which allows to take advantage of the high degree of redundancy of natural images. Furthermore, we discuss the main challenges of the nonlocal regularization to create efficient numerical solvers which occurs automatically due to the high structure of complexity of the nonlocal regularization graph.

  13. Monitoring intracellular polyphosphate accumulation in enhanced biological phosphorus removal systems by quantitative image analysis.

    Science.gov (United States)

    Mesquita, Daniela P; Amaral, A Luís; Leal, Cristiano; Carvalheira, Mónica; Cunha, Jorge R; Oehmen, Adrian; Reis, Maria A M; Ferreira, Eugénio C

    2014-01-01

    A rapid methodology for intracellular storage polyphosphate (poly-P) identification and monitoring in enhanced biological phosphorus removal (EBPR) systems is proposed based on quantitative image analysis (QIA). In EBPR systems, 4',6-diamidino-2-phenylindole (DAPI) is usually combined with fluorescence in situ hybridization to evaluate the microbial community. The proposed monitoring technique is based on a QIA procedure specifically developed for determining poly-P inclusions within a biomass suspension using solely DAPI by epifluorescence microscopy. Due to contradictory literature regarding DAPI concentrations used for poly-P detection, the present work assessed the optimal DAPI concentration for samples acquired at the end of the EBPR aerobic stage when the accumulation occurred. Digital images were then acquired and processed by means of image processing and analysis. A correlation was found between average poly-P intensity values and the analytical determination. The proposed methodology can be seen as a promising alternative procedure for quantifying intracellular poly-P accumulation in a faster and less labour-intensive way.

  14. Ways of incorporating photographic images in learning and assessing high school biology: A study of visual perception and visual cognition

    Science.gov (United States)

    Nixon, Brenda Chaumont

    This study evaluated the cognitive benefits and costs of incorporating biology-textbook and student-generated photographic images into the learning and assessment processes within a 10th grade biology classroom. The study implemented Wandersee's (2000) 20-Q Model of Image-Based Biology Test-Item Design (20-Q Model) to explore the use of photographic images to assess students' understanding of complex biological processes. A thorough review of the students' textbook using ScaleMaster R with PC Interface was also conducted. The photographs, diagrams, and other representations found in the textbook were measured to determine the percentage of each graphic depicted in the book and comparisons were made to the text. The theoretical framework that guided the research included Human Constructivist tenets espoused by Mintzes, Wandersee and Novak (2000). Physiological and cognitive factors of images and image-based learning as described by Robin (1992), Solso (1997) and Wandersee (2000) were examined. Qualitative case study design presented by Yin (1994), Denzin and Lincoln (1994) was applied and data were collected through interviews, observations, student activities, student and school artifacts and Scale Master IIRTM measurements. The results of the study indicate that although 24% of the high school biology textbook is devoted to photographic images which contribute significantly to textbook cost, the teacher and students paid little attention to photographic images other than as aesthetic elements for creating biological ambiance, wasting valuable opportunities for learning. The analysis of the photographs corroborated findings published by the Association American Association for the Advancement of Science that indicated "While most of the books are lavishly illustrated, these representations are rarely helpful, because they are too abstract, needlessly complicated, or inadequately explained" (Roseman, 2000, p. 2). The findings also indicate that applying the 20-Q

  15. Vocabulary Length Experiments for Binary Image Classification Using BOV Approach

    Directory of Open Access Journals (Sweden)

    S.P.Vimal

    2013-12-01

    Full Text Available Bag-of-Visual-words (BoV approach to image classif ication is popular among computer vision scientists . The visual words come from the visual vocabulary wh ich is constructed using the key points extracted f rom the image database. Unlike the natural language, th e length of such vocabulary for image classificatio n is task dependent. The visual words capture the local invariant features of the image. The region of imag e over which a visual word is constrained forms the s patial content for the visual word. Spatial pyramid representation of images is an approach to handle s patial information. In this paper, we study the rol e of vocabulary lengths for the levels of a simple two l evel spatial pyramid to perform binary classificati ons. Two binary classification problems namely to detect the presence of persons and cars are studied. Rele vant images from PASCAL dataset are being used for the l earning activities involved in this work

  16. Horse Manure and Other Fun Projects. Field Studies and Laboratory Experiences in Environmental Biology - A Book of Experimental Ideas for Secondary School Biology Teachers.

    Science.gov (United States)

    Brown, Robert T., Ed.; Clark, Barbara G., Ed.

    This guide contains a collection of laboratory and field inquiries designed to promote ecological awareness, sensitivity, and understanding. The activities compiled by 28 teachers are for use in teaching biology at the secondary level. They are presented in a "recipe" form to make it possible for teachers without prior experience or training to…

  17. MR imaging of prostate. Preliminary experience with calculated imaging in 28 cases

    Energy Technology Data Exchange (ETDEWEB)

    Gevenois, P.A.; Van Regemorter, G.; Ghysels, M.; Delepaut, A.; Van Gansbeke, D.; Struyven, J.

    1988-04-01

    The majority of studies with MR imaging in prostate disease are based on a semiology obtained using images weighted in T1 and T2. A study was carried out to evaluate effects of images calculated in T1 and T2 obtained at 0.5T. This preliminary study concerns 28 prostate examinations with spin-echo acquisition and inversion-recuperation parameters, and provided images calculated in T1, weighted and calculated in T2. Images allowed detection and characterization of prostate lesions. However, although calculated images accentuate discrimination of the method, the weighted images conserve their place because of their improved spatial resolution.

  18. Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Son N.; Liyu, Andrey V.; Chu, Rosalie K.; Anderton, Christopher R.; Laskin, Julia

    2017-01-17

    A new approach for constant distance mode mass spectrometry imaging of biological samples using nanospray desorption electrospray ionization (nano-DESI MSI) was developed by integrating a shear-force probe with nano-DESI probe. The technical concept and basic instrumental setup as well as general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enables constant-distance imaging mode via a computer controlled closed feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus Subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites including non-ribosomal peptides (surfactin, plipastatin and iturin) and iron-bound heme on the surface of living bacterial colonies ranging in diameter from 10 mm to 13 mm with height variations of up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Constant-mode nano-DESI MSI is ideally suited for imaging biological samples of complex topography in their native state.

  19. Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography.

    Science.gov (United States)

    Nguyen, Son N; Liyu, Andrey V; Chu, Rosalie K; Anderton, Christopher R; Laskin, Julia

    2017-01-17

    A new approach for constant-distance mode mass spectrometry imaging (MSI) of biological samples using nanospray desorption electrospray ionization (nano-DESI) was developed by integrating a shear-force probe with the nano-DESI probe. The technical concept and basic instrumental setup, as well as the general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enabled the constant-distance imaging mode via a computer-controlled closed-feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites, including nonribosomal peptides (surfactin, plipastatin, and iturin) on the surface of living bacterial colonies, ranging in diameter from 10 to 13 mm, with height variations up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Based on this effort, constant-mode nano-DESI MSI proved to be ideally suited for imaging biological samples of complex topography in their native states.

  20. Do medical images aid understanding and recall of medical information? An experimental study comparing the experience of viewing no image, a 2D medical image and a 3D medical image alongside a diagnosis.

    Science.gov (United States)

    Phelps, Emma Elizabeth; Wellings, Richard; Griffiths, Frances; Hutchinson, Charles; Kunar, Melina

    2017-06-01

    This study compared the experience of viewing 3D medical images, 2D medical images and no image presented alongside a diagnosis. We conducted two laboratory experiments, each with 126 healthy participants. Participants heard three diagnoses; one accompanied by 3D medical images, one accompanied by 2D medical images and one with no image. Participants completed a questionnaire after each diagnosis rating their experience. In Experiment 2, half of the participants were informed that image interpretation can be susceptible to errors. Participants preferred to view 3D images alongside a diagnosis (pmedical images may aid patient understanding, recall and trust in medical information. Medical images may be a powerful resource for patients that could be utilised by clinicians during consultations. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. Biological properties of 2'-[18F]fluoroflumazenil for central benzodiazepine receptor imaging.

    Science.gov (United States)

    Chang, Young Soo; Jeong, Jae Min; Yoon, Young Hyun; Kang, Won Jun; Lee, Seung Jin; Lee, Dong Soo; Chung, June-Key; Lee, Myung Chul

    2005-04-01

    A novel positron emitting agent, 2'-[18F]fluoroflumazenil (fluoroethyl 8-fluoro-5-methyl-6-oxo-5,6-dihydro-4H-benzo-[f]imidazo[1,5-a][1,4]diazepine-3-carboxylate, FFMZ), has been reported for benzodiazepine imaging. In the present study, biological properties of [18F]FFMZ were investigated. Stability tests of [18F]FFMZ in human and rat sera were performed. Biodistribution was investigated in mice and phosphorimages of brains were obtained from rats. A receptor binding assay was performed using rat brain (mixture of cortex and cerebellum) homogenate. A static positron emission tomography (PET) image was obtained from a normal human volunteer. Although [18F]FFMZ was stable in human serum, it was rapidly hydrolyzed in rat serum. The hydrolysis was 39%, 63% and 92% at 10, 30 and 60 min, respectively. According to the biodistribution study in mice, somewhat even distribution (between 2 approximately 3% ID/g) was observed in most organs. Intestinal uptake increased up to 6% ID/g at 1 h due to biliary excretion. Bone uptake slowly increased from 1.5% to 3.5% ID/g at 1 h. High uptakes in the cortex, thalamus and cerebellum, which could be completely blocked by coinjection of cold FMZ, were observed by phosphorimaging study using rats. Determination of Kd value and Bmax using rat brain tissue was performed by Scatchard plotting and found 1.45+/-0.26 nM and 1.08+/-0.03 pmol/mg protein, respectively. The PET image of the normal human volunteer showed high uptake in the following decreasing order: frontal cortex, temporal cortex, occipital cortex, cerebellum, parietal cortex and thalamus. In conclusion, the new FMZ derivative, [18F]FFMZ appears to be a promising PET agent for central benzodiazepine receptor imaging with a convenient labeling procedure and a specific binding property.

  2. Nuclear imaging of the fuel assembly in ignition experiments

    Energy Technology Data Exchange (ETDEWEB)

    Grim, G. P.; Guler, N.; Merrill, F. E.; Morgan, G. L.; Danly, C. R.; Volegov, P. L.; Wilde, C. H.; Wilson, D. C.; Clark, D. S.; Hinkel, D. E.; Jones, O. S.; Raman, K. S.; Izumi, N.; Fittinghoff, D. N.; Drury, O. B.; Alger, E. T.; Arnold, P. A.; Ashabranner, R. C.; Atherton, L. J.; Barrios, M. A.; Batha, S.; Bell, P. M.; Benedetti, L. R.; Berger, R. L.; Bernstein, L. A.; Berzins, L. V.; Betti, R.; Bhandarkar, S. D.; Bionta, R. M.; Bleuel, D. L.; Boehly, T. R.; Bond, E. J.; Bowers, M. W.; Bradley, D. K.; Brunton, G. K.; Buckles, R. A.; Burkhart, S. C.; Burr, R. F.; Caggiano, J. A.; Callahan, D. A.; Casey, D. T.; Castro, C.; Celliers, P. M.; Cerjan, C. J.; Chandler, G. A.; Choate, C.; Cohen, S. J.; Collins, G. W.; Cooper, G. W.; Cox, J. R.; Cradick, J. R.; Datte, P. S.; Dewald, E. L.; Di Nicola, P.; Di Nicola, J. M.; Divol, L.; Dixit, S. N.; Dylla-Spears, R.; Dzenitis, E. G.; Eckart, M. J.; Eder, D. C.; Edgell, D. H.; Edwards, M. J.; Eggert, J. H.; Ehrlich, R. B.; Erbert, G. V.; Fair, J.; Farley, D. R.; Felker, B.; Fortner, R. J.; Frenje, J. A.; Frieders, G.; Friedrich, S.; Gatu-Johnson, M.; Gibson, C. R.; Giraldez, E.; Glebov, V. Y.; Glenn, S. M.; Glenzer, S. H.; Gururangan, G.; Haan, S. W.; Hahn, K. D.; Hammel, B. A.; Hamza, A. V.; Hartouni, E. P.; Hatarik, R.; Hatchett, S. P.; Haynam, C.; Hermann, M. R.; Herrmann, H. W.; Hicks, D. G.; Holder, J. P.; Holunga, D. M.; Horner, J. B.; Hsing, W. W.; Huang, H.; Jackson, M. C.; Jancaitis, K. S.; Kalantar, D. H.; Kauffman, R. L.; Kauffman, M. I.; Khan, S. F.; Kilkenny, J. D.; Kimbrough, J. R.; Kirkwood, R.; Kline, J. L.; Knauer, J. P.; Knittel, K. M.; Koch, J. A.; Kohut, T. R.; Kozioziemski, B. J.; Krauter, K.; Krauter, G. W.; Kritcher, A. L.; Kroll, J.; Kyrala, G. A.; Fortune, K. N. La; LaCaille, G.; Lagin, L. J.; Land, T. A.; Landen, O. L.; Larson, D. W.; Latray, D. A.; Leeper, R. J.; Lewis, T. L.; LePape, S.; Lindl, J. D.; Lowe-Webb, R. R.; Ma, T.; MacGowan, B. J.; MacKinnon, A. J.; MacPhee, A. G.; Malone, R. M.; Malsbury, T. N.; Mapoles, E.; Marshall, C. D.; Mathisen, D. G.; McKenty, P.; McNaney, J. M.; Meezan, N. B.; Michel, P.; Milovich, J. L.; Moody, J. D.; Moore, A. S.; Moran, M. J.; Moreno, K.; Moses, E. I.; Munro, D. H.; Nathan, B. R.; Nelson, A. J.; Nikroo, A.; Olson, R. E.; Orth, C.; Pak, A. E.; Palma, E. S.; Parham, T. G.; Patel, P. K.; Patterson, R. W.; Petrasso, R. D.; Prasad, R.; Ralph, J. E.; Regan, S. P.; Rinderknecht, H.; Robey, H. F.; Ross, G. F.; Ruiz, C. L.; Seguin, F. H.; Salmonson, J. D.; Sangster, T. C.; Sater, J. D.; Saunders, R. L.; Schneider, M. B.; Schneider, D. H.; Shaw, M. J.; Simanovskaia, N.; Spears, B. K.; Springer, P. T.; Stoeckl, C.; Stoeffl, W.; Suter, L. J.; Thomas, C. A.; Tommasini, R.; Town, R. P.; Traille, A. J.; Wonterghem, B. Van; Wallace, R. J.; Weaver, S.; Weber, S. V.; Wegner, P. J.; Whitman, P. K.; Widmann, K.; Widmayer, C. C.; Wood, R. D.; Young, B. K.; Zacharias, R. A.; Zylstra, A.

    2013-05-01

    First results from the analysis of neutron image data collected on implosions of cryogenically layered deuterium-tritium capsules during the 2011-2012 National Ignition Campaign are reported. The data span a variety of experimental designs aimed at increasing the stagnation pressure of the central hotspot and areal density of the surrounding fuel assembly. Images of neutrons produced by deuterium–tritium fusion reactions in the hotspot are presented, as well as images of neutrons that scatter in the surrounding dense fuel assembly. The image data are compared with 1D and 2D model predictions, and consistency checked using other diagnostic data. The results indicate that the size of the fusing hotspot is consistent with the model predictions, as well as other imaging data, while the overall size of the fuel assembly, inferred from the scattered neutron images, is systematically smaller than models’ prediction. Preliminary studies indicate these differences are consistent with a significant fraction (20%–25%) of the initial deuterium-tritium fuel mass outside the compact fuel assembly, due either to low mode mass asymmetry or high mode 3D mix effects at the ablator-ice interface.

  3. Experience With Intravascular Ultrasound Imaging Of Human Atherosclerotic Arteries

    Science.gov (United States)

    Mallery, John A.; Gessert, James M.; Maciel, Mario; Tobis, John M.; Griffith, James M.; Berns, Michael W.; Henry, Walter L.

    1989-08-01

    Normal human arteries have a well-defined structure on intravascular images. The intima appears very thin and is most likely represented by a bright reflection arising from the internal elastic lamina. The smooth muscle tunica media is echo-lucent on the ultrasound image and appears as a dark band separating the intima from the adventitia. The adventitia is a brightly reflective layer of variable thickness. The thickness of the intima, and therefore of the atherosclerotic plaque can be accurately measured from the ultrasound images and correlates well with histology. Calcification within the wall of arteries is seen as bright echo reflection with shadowing of the peripheral wall. Fibrotic regions are highly reflective but do not shadow. Necrotic liquid regions within advanced atherosclerotic plaques are seen on ultrasound images as large lucent zones surrounded by echogenic tissue. Imaging can be performed before and after interventional procedures, such as laser angioplasty, balloon angioplasty and atherectomy. Intravascular ultrasound appears to provide an imaging modality for identifying the histologic characteristics of diseased arteries and for quantifying plaque thickness. It might be possible to perform such quantification to evaluate the results of interventional procedures.

  4. Experiment design through dynamical characterisation of non-linear systems biology models utilising sparse grids.

    Science.gov (United States)

    Donahue, M M; Buzzard, G T; Rundell, A E

    2010-07-01

    The sparse grid-based experiment design algorithm sequentially selects an experimental design point to discriminate between hypotheses for given experimental conditions. Sparse grids efficiently screen the global uncertain parameter space to identify acceptable parameter subspaces. Clustering the located acceptable parameter vectors by the similarity of the simulated model trajectories characterises the data-compatible model dynamics. The experiment design algorithm capitalizes on the diversity of the experimentally distinguishable system output dynamics to select the design point that best discerns between competing model-structure and parameter-encoded hypotheses. As opposed to designing the experiments to explicitly reduce uncertainty in the model parameters, this approach selects design points to differentiate between dynamical behaviours. This approach further differs from other experimental design methods in that it simultaneously addresses both parameter- and structural-based uncertainty that is applicable to some ill-posed problems where the number of uncertain parameters exceeds the amount of data, places very few requirements on the model type, available data and a priori parameter estimates, and is performed over the global uncertain parameter space. The experiment design algorithm is demonstrated on a mitogen-activated protein kinase cascade model. The results show that system dynamics are highly uncertain with limited experimental data. Nevertheless, the algorithm requires only three additional experimental data points to simultaneously discriminate between possible model structures and acceptable parameter values. This sparse grid-based experiment design process provides a systematic and computationally efficient exploration over the entire uncertain parameter space of potential model structures to resolve the uncertainty in the non-linear systems biology model dynamics.

  5. Update in Molecular Biology for Teachers from Public Schools: a Knowledge Exchange Experience.

    Directory of Open Access Journals (Sweden)

    C.R. Córdula

    2009-05-01

    Full Text Available One  of the goals of the graduate Program in Molecular Biology from UNIFESP (PrMB -UNIFESP is to contribute for continuing education of biology teachers from public high schools. A close relation between university and public schools is an important channel for dissemination of scientific knowledge. Thus, a 40h Molecular Biology updating course was offered to 20 high school teachers. The objective was to discuss genomic and proteomic advances and their application. The course was organized by graduate students  from PrMB -UNIFESP. Three groups ofstudents were formed, two being responsible for theorical and practical classes and one for global logistic including searching for financial support. The themes presented to the teachers were flow of genetic information,  recombinant DNA, gene cloning, transgenic plants and animals, mutation, super bacteria and stem cell. The teachers also had hands-on classes including DNA extraction, PCR, gene cloning and SDS-PAGE. The teachers received an assignment to go back to their s chools and do some activity with their students that would be related to the themes discussed. The students produced videos, discussions, posters, theater, experimental models and pratical classes related to the course themes. After 3 months the teachers r eturned to show their students’ work.  We conclude that information was transmitted to the teachers, updating them, and to high school students, that learned science in a entertaining way. Also, the graduate students had an experience on how to organize a c ourse including all its responsibilities.

  6. Carbon nanotubes allow capture of krypton, barium and lead for multichannel biological X-ray fluorescence imaging

    Science.gov (United States)

    Serpell, Christopher J.; Rutte, Reida N.; Geraki, Kalotina; Pach, Elzbieta; Martincic, Markus; Kierkowicz, Magdalena; de Munari, Sonia; Wals, Kim; Raj, Ritu; Ballesteros, Belén; Tobias, Gerard; Anthony, Daniel C.; Davis, Benjamin G.

    2016-10-01

    The desire to study biology in situ has been aided by many imaging techniques. Among these, X-ray fluorescence (XRF) mapping permits observation of elemental distributions in a multichannel manner. However, XRF imaging is underused, in part, because of the difficulty in interpreting maps without an underlying cellular `blueprint' this could be supplied using contrast agents. Carbon nanotubes (CNTs) can be filled with a wide range of inorganic materials, and thus can be used as `contrast agents' if biologically absent elements are encapsulated. Here we show that sealed single-walled CNTs filled with lead, barium and even krypton can be produced, and externally decorated with peptides to provide affinity for sub-cellular targets. The agents are able to highlight specific organelles in multiplexed XRF mapping, and are, in principle, a general and versatile tool for this, and other modes of biological imaging.

  7. Workshop on "What do you need to know about doing cell biology experiments in space?".

    Science.gov (United States)

    2004-03-01

    The "What do you need to know about doing cell biology experiments in space?" workshop represented a continued international collaboration between cell culture hardware developers and scientists, partly due to the enhanced collaboration in space life sciences spurred on by the International Space Life Sciences Working Group. The workshop was organized into three sessions. The first session provided an overview of the general effects of space flight, including definition of the microgravity environment, the radiation environment, and issues surrounding mass transport. The session concluded with an important overview of using space centrifuges as Earth gravity (1-g) controls, including understanding the contribution of inertial shear forces. The second session described existing and planned hardware facilities developed to support cell culture research, ranging from small hand-held hardware to breadbox-sized Shuttle middeck hardware to complete facility racks. Hardware designed for use on the Shuttle, ISS, and in free flyers was described. The third session provided advice from experienced space flight cell biology principal investigators to new investigators in the field. This special issue of the Journal of Gravitational Physiology includes externally peer-reviewed papers from all three sessions.

  8. Insect gravitational biology: ground-based and shuttle flight experiments using the beetle Tribolium castaneum

    Science.gov (United States)

    Bennett, R. L.; Abbott, M. K.; Denell, R. E.; Spooner, B. S. (Principal Investigator)

    1994-01-01

    Many of the traditional experimental advantages of insects recommend their use in studies of gravitational and space biology. The fruit fly, Drosophila melanogaster, is an obvious choice for studies of the developmental significance of gravity vectors because of the unparalleled description of regulatory mechanisms controlling oogenesis and embryogenesis. However, we demonstrate that Drosophila could not survive the conditions mandated for particular flight opportunities on the Space Shuttle. With the exception of Drosophila, the red flour beetle, Tribolium castaneum, is the insect best characterized with respect to molecular embryology and most frequently utilized for past space flights. We show that Tribolium is dramatically more resistant to confinement in small sealed volumes. In preparation for flight experiments we characterize the course and timing of the onset of oogenesis in newly eclosed adult females. Finally, we present results from two shuttle flights which indicate that a number of aspects of the development and function of the female reproductive system are not demonstrably sensitive to microgravity. Available information supports the utility of this insect for future studies of gravitational biology.

  9. Semi-automated operation of Mars Climate Simulation chamber - MCSC modelled for biological experiments

    Science.gov (United States)

    Tarasashvili, M. V.; Sabashvili, Sh. A.; Tsereteli, S. L.; Aleksidze, N. D.; Dalakishvili, O.

    2017-10-01

    The Mars Climate Simulation Chamber (MCSC) (GEO PAT 12 522/01) is designed for the investigation of the possible past and present habitability of Mars, as well as for the solution of practical tasks necessary for the colonization and Terraformation of the Planet. There are specific tasks such as the experimental investigation of the biological parameters that allow many terrestrial organisms to adapt to the imitated Martian conditions: chemistry of the ground, atmosphere, temperature, radiation, etc. MCSC is set for the simulation of the conduction of various biological experiments, as well as the selection of extremophile microorganisms for the possible Settlement, Ecopoesis and/or Terraformation purposes and investigation of their physiological functions. For long-term purposes, it is possible to cultivate genetically modified organisms (e.g., plants) adapted to the Martian conditions for future Martian agriculture to sustain human Mars missions and permanent settlements. The size of the chamber allows preliminary testing of the functionality of space-station mini-models and personal protection devices such as space-suits, covering and building materials and other structures. The reliability of the experimental biotechnological materials can also be tested over a period of years. Complex and thorough research has been performed to acquire the most appropriate technical tools for the accurate engineering of the MCSC and precious programmed simulation of Martian environmental conditions. This paper describes the construction and technical details of the equipment of the MCSC, which allows its semi-automated, long-term operation.

  10. Biological image construction by using Raman radiation and Pca: preliminary results

    Energy Technology Data Exchange (ETDEWEB)

    Martinez E, J. C. [IPN, Unidad Profesional Interdisciplinaria de Ingenieria, Campus Guanajuato, Av. Mineral de Valenciana 200, Col. Fracc. Industrial Puerto Interior, 36275 Silao, Guanajuato (Mexico); Cordova F, T. [Universidad de Guanajuato, DIC, Departamento de Ingenieria Fisica, Loma del Bosque No. 103, Col. Lomas del Campestre, 37150 Leon, Guanajuato (Mexico); Hugo R, V., E-mail: jcmartineze@ipn.mx [Universidad de Guadalajara, Centro Universitario de Tonala, Morelos No. 180, 69584 Tonala, Jalisco (Mexico)

    2015-10-15

    Full text: In the last years, the Raman spectroscopy (Rs) technique has had some applications in the study and analysis of biological samples, due to it is able to detect concentrations or presence of certain organic and inorganic compounds of medical interest. In this work, raw data were obtained through measurements in selected points on a square regions in order to detect specific organic / inorganic compounds on biological samples. Gold nano stars samples were prepared and coated with membrane markers (CD 10+ and CD 19+) and diluted in leukemic B lymphocytes. Each data block was evaluated independently by the method of principal component analysis (Pca) in order to find representative dimensionless values (Cp) for each Raman spectrum in a specific coordinate. Each Cp was normalized in a range of 0-255 in order to generate a representative image of 8 bits of the region under study. Data acquisition was performed with Raman microscopy system Renishaw in Via in the range of 550 to 1700 cm-1 with a 785 nm laser source, with a power of 17 m W and 15 s of exposure time were used for each spectrum. In preliminary results could detect the presence of molecular markers CD 10+ and CD 19+ with gold nano stars and discrimination between both markers. The results suggest conducting studies with specific concentrations organic and inorganic materials. (Author)

  11. Heroin abuse accelerates biological aging: a novel insight from telomerase and brain imaging interaction.

    Science.gov (United States)

    Cheng, G L F; Zeng, H; Leung, M-K; Zhang, H-J; Lau, B W M; Liu, Y-P; Liu, G-X; Sham, P C; Chan, C C H; So, K-F; Lee, T M C

    2013-05-21

    Heroin abuse and natural aging exert common influences on immunological cell functioning. This observation led to a recent and untested idea that aging may be accelerated in abusers of heroin. We examined this claim by testing whether heroin use is associated with premature aging at both cellular and brain system levels. A group of abstinent heroin users (n=33) and matched healthy controls (n=30) were recruited and measured on various biological indicators of aging. These measures included peripheral blood telomerase activity, which reflects cellular aging, and both structural and functional measures of brain magnetic resonance imaging. We found that heroin users were characterized by significantly low telomerase activity (0.21 vs 1.78; 88% reduction; t(61)=6.96, Pbrain region implicated in aging. Using the PFC location identified from the structural analyses as a 'seed' region, it was further revealed that telomerase activity interacted with heroin use to impact age-sensitive brain functional networks (AlphaSim corrected Pbrain system and behavioral measures in the context of substance abuse. The present finding that heroin abuse is associated with accelerated aging at both cellular and brain system levels is novel and forms a unique contribution to our knowledge in how the biological processes of drug abusers may be disrupted.

  12. Studying Biological Tissue with Fluorescence Lifetime Imaging: Microscopy, Endoscopy, and Complex Decay Profiles

    Science.gov (United States)

    Siegel, Jan; Elson, Daniel S.; Webb, Stephen E. D.; Lee, K. C. Benny; Vlandas, Alexis; Gambaruto, Giovanni L.; Léveque-Fort, Sandrine; Lever, M. John; Tadrous, Paul J.; Stamp, Gordon W. H.; Wallace, Andrew L.; Sandison, Ann; Watson, Tim F.; Alvarez, Fernando; French, Paul M. W.

    2003-06-01

    We have applied fluorescence lifetime imaging (FLIM) to the autofluorescence of different kinds of biological tissue in vitro , including animal tissue sections and knee joints as well as human teeth, obtaining two-dimensional maps with functional contrast. We find that fluorescence decay profiles of biological tissue are well described by the stretched exponential function (StrEF), which can represent the complex nature of tissue. The StrEF yields a continuous distribution of fluorescence lifetimes, which can be extracted with an inverse Laplace transformation, and additional information is provided by the width of the distribution. Our experimental results from FLIM microscopy in combination with the StrEF analysis indicate that this technique is ready for clinical deployment, including portability that is through the use of a compact picosecond diode laser as the excitation source. The results obtained with our FLIM endoscope successfully demonstrated the viability of this modality, though they need further optimization. We expect a custom-designed endoscope with optimized illumination and detection efficiencies to provide significantly improved performance.

  13. Evidence of disorder in biological molecules from single molecule pulling experiments

    CERN Document Server

    Hyeon, Changbong; Thirumalai, D

    2014-01-01

    Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an exactly solvable model in which the unfolding rate due to mechanical force depends parametrically on an auxiliary variable representing an entropy barrier arising from fluctuations in internal dynamics. When the rate of fluctuations, a measure of dynamical disorder, is comparable to or smaller than the rate of force-induced unbinding, we show that there are two experimentally observable consequences: non-exponential survival probability at constant force, and a heavy-tailed rupture force distribution at constant loading rate. By fitting our analytical expressions to data from single molecule pulling experiments on proteins and DNA, we quantify the extent of disorder. We show that only by analyzing data over a wide range of forces and loading rates can the role of disorder due...

  14. Electrophoresis tests on STS-3 and ground control experiments - A basis for future biological sample selections

    Science.gov (United States)

    Morrison, D. R.; Lewis, M. L.

    1982-01-01

    Static zone electrophoresis is an electrokinetic method of separating macromolecules and small particles. However, its application for the isolation of biological cells and concentrated protein solutions is limited by sedimentation and convection. Microgravity eliminates or reduces sedimentation, floatation, and density-driven convection arising from either Joule heating or concentration differences. The advantages of such an environment were first demonstrated in space during the Apollo 14 and 16 missions. In 1975 the Electrophoresis Technology Experiment (MA-011) was conducted during the Apollo-Soyuz Test Project flight. In 1979 a project was initiated to repeat the separations of human kidney cells. One of the major objectives of the Electrophoresis Equipment Verification Tests (EEVT) on STS-3 was to repeat and thereby validate the first successful electrophoretic separation of human kidney cells. Attention is given to the EEVT apparatus, the preflight electrophoresis, and inflight operational results.

  15. Biological welfare and the commons: A natural experiment in the Alps, 1765-1845.

    Science.gov (United States)

    O'Grady, Trevor; Tagliapietra, Claudio

    2017-06-06

    In the late 18th century hundreds self-governing alpine communities in Northern Italy came under the direct control of centralized states (Austria and France) at different times. We exploit the timing and location of these interventions in a difference-in-differences type design to investigate the effects of removing CPR (common-pool resources) institutions on biological welfare. We find a significant and persistent increase in infant mortality rates and a more modest decrease in birth rates as a result of state centralization. We provide evidence that these demographic changes reflect a critical loss of natural resource income caused by the disruption of communal institutions. Impacts are most severe in communities that have no prior experience with formal institutions. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. CHANGES IN BIOLOGICAL PROPERTIES OF ORDINARY BLACK SOILS AT GLEYISATION (MODEL EXPERIMENT

    Directory of Open Access Journals (Sweden)

    Kandashova K. A.

    2015-10-01

    Full Text Available The article presents the results of laboratory modeling of gleyisation and its effect on the biological properties of soils with stagnant regime in ordinary black soils. Gleyisation is a complex biochemical process that occurs under oxygen reduction conditions. Anaerobic microorganisms, the presence of organic substances, and the constant or prolonged waterlogging of individual horizons or the entire soil profile promote gleyisation. Model experiments revealed that gleyisation increase the total number of bacteria and suppresses number of actinomycetes, micromycetes and growth of fungal mycelium. Gleyisation decreases the activity of oxidoreductases and increases the hydrolases activity. In addition, the second content of humus slightly increases and active acidity (pH changes to neutral. Accumulation of large amounts of iron oxide (II in soil is revealed

  17. Biological stress indicators as risk markers for increased alcohol use following traumatic experiences.

    Science.gov (United States)

    Trautmann, Sebastian; Muehlhan, Markus; Kirschbaum, Clemens; Wittchen, Hans-Ulrich; Höfler, Michael; Stalder, Tobias; Steudte-Schmiedgen, Susann

    2017-01-20

    Alcohol misuse is a common sequela of traumatic event experiences causing considerable morbidity and mortality. Although biological stress indicators have been identified as useful risk markers for the development of trauma-related disorders, no such biological indicators exist for the risk of increased alcohol use after trauma exposure. This is the first study to prospectively investigate the predictive value of long-term cortisol levels and acute stress reactivity for the risk of increased alcohol use following traumatic events. Male soldiers were examined before and 12 months following deployment using a standardized diagnostic interview. We analyzed the moderating role of baseline hair cortisol concentrations (HCCs, n = 153) as well as baseline salivary cortisol and alpha-amylase stress reactivity in response to a laboratory stressor (n = 145) in the association between new-onset traumatic events (according to the DSM-IV A1 criterion) and subsequent daily alcohol use. No main effects of pre-traumatic HCC or salivary stress markers on subsequent change in alcohol use were observed. However, we found that with decreasing HCC, the number of new-onset traumatic events was more strongly associated with subsequent alcohol use independent from changes in posttraumatic stress disorder symptoms. No such relation was seen for the acute stress reactivity data. Taken together, this study provides first evidence suggesting that individual differences in long-term cortisol regulation are involved in the association between traumatic experiences and subsequent alcohol use. HCC may thus serve as a potential target in the early identification of individuals vulnerable for increased alcohol use following traumatic events. © 2017 Society for the Study of Addiction.

  18. Resolution criteria in double-slit microscopic imaging experiments

    Science.gov (United States)

    You, Shangting; Kuang, Cuifang; Zhang, Baile

    2016-09-01

    Double-slit imaging is widely used for verifying the resolution of high-resolution and super-resolution microscopies. However, due to the fabrication limits, the slit width is generally non-negligible, which can affect the claimed resolution. In this paper we theoretically calculate the electromagnetic field distribution inside and near the metallic double slit using waveguide mode expansion method, and acquire the far-field image by vectorial Fourier optics. We find that the slit width has minimal influence when the illuminating light is polarized parallel to the slits. In this case, the claimed resolution should be based on the center-to-center distance of the double-slit.

  19. Our Experience with MR Imaging of Perianal Fistulas

    Science.gov (United States)

    Baskan, Ozdil; Koplay, Mustafa; Sivri, Mesut; Erol, Cengiz

    2014-01-01

    Summary Magnetic resonance imaging (MRI) depicts infectious foci in the perianal region better than any other imaging modality. MRI allows definition of the fistula, associated abscess formation and its secondary extensions. Accurate information is necessary for surgical treatment and to obtain a decrease in the incidence of recurrence and complications. Radiologists should be familiar with anatomical and pathological findings of perianal fistulas and classify them using the MRI – based grading system. The purpose of this article was to provide an overview for evaluation of perianal fistulas, examples of various fistula types and their classification. PMID:25550766

  20. Computer image processing - The Viking experience. [digital enhancement techniques

    Science.gov (United States)

    Green, W. B.

    1977-01-01

    Computer processing of digital imagery from the Viking mission to Mars is discussed, with attention given to subjective enhancement and quantitative processing. Contrast stretching and high-pass filtering techniques of subjective enhancement are described; algorithms developed to determine optimal stretch and filtering parameters are also mentioned. In addition, geometric transformations to rectify the distortion of shapes in the field of view and to alter the apparent viewpoint of the image are considered. Perhaps the most difficult problem in quantitative processing of Viking imagery was the production of accurate color representations of Orbiter and Lander camera images.

  1. Diffuse reflectance spectroscopy and optical polarization imaging of in-vivo biological tissue

    Science.gov (United States)

    Mora-Núñez, A.; Castillejos, Y.; García-Torales, G.; Martínez-Ponce, G.

    2013-11-01

    A number of optical techniques have been reported in the scientific literature as accomplishable methodologies to diagnose diseases in biological tissue, for instance, diffuse reflectance spectroscopy (DRS) and optical polarization imaging (OPI). The skin is the largest organ in the body and consists of three primary layers, namely, the epidermis (the outermost layer exposed to the world), the dermis, and the hypodermis. The epidermis changes from to site to site, mainly because of difference in hydration. A lower water content increase light scattering and reduce the penetration depth of radiation. In this work, two hairless mice have been selected to evaluate their skin features by using DRS and OPI. Four areas of the specimen body were chosen to realize the comparison: back, abdomen, tail, and head. From DRS, it was possible to distinguish the skin nature because of different blood irrigation at dermis. In the other hand, OPI shows pseudo-depolarizing regions in the measured Mueller images related to a spatially varying propagation of the scattered light. This provides information about the cell size in the irradiated skin.

  2. Imaging of the World's Fastest Biological Spring Vorticella Convallaria Via Atomic Force Micoscopy

    Science.gov (United States)

    Bras, Rafael; Upadhyaya, Arpita; van Oudenaarden, Alexander; Ortiz, Christine

    2002-03-01

    The rod-like, contractile stalk (25-300 micron length, 4 micron diameter) of the single-celled peritrich Vorticella Convallaria can collapse into a tightly coiled helix in > 1/60 second. The stalk consists of membranes stiffened by an assembly of protein bundles (batonets) surrounding the spasmoneme, an asymmetrically located bundle of negatively charged polyelectrolytic spasmin protein. It is thought that contraction results from the entropic collapse of spasmin via Ca2+ screening of electrostatic repulsion. After culturing, an aqueous solution containing detached cells was filtered and placed on freshly cleaved mica substrates to dry in air for 30min. The samples were imaged via contact mode atomic force microscopy. The following was clearly visualized; the helicity of the stalk, the spasmonene (1.3-2.4 micron diameter), batonets (230-300nm), the outer stalk membrane morphology, and organelles in the stalk. The circular stalk "foot" (2.8 micron diameter) where the organism attached itself to substrates was also imaged, which may be the biological "glue" used for surface attachment.

  3. Body Image in Anorexia Nervosa: Body Size Estimation Utilising a Biological Motion Task and Eyetracking.

    Science.gov (United States)

    Phillipou, Andrea; Rossell, Susan Lee; Gurvich, Caroline; Castle, David Jonathan; Troje, Nikolaus Friedrich; Abel, Larry Allen

    2016-03-01

    Anorexia nervosa (AN) is a psychiatric condition characterised by a distortion of body image. However, whether individuals with AN can accurately perceive the size of other individuals' bodies is unclear. In the current study, 24 women with AN and 24 healthy control participants undertook two biological motion tasks while eyetracking was performed: to identify the gender and to indicate the walkers' body size. Anorexia nervosa participants tended to 'hyperscan' stimuli but did not demonstrate differences in how visual attention was directed to different body areas, relative to controls. Groups also did not differ in their estimation of body size. The hyperscanning behaviours suggest increased anxiety to disorder-relevant stimuli in AN. The lack of group difference in the estimation of body size suggests that the AN group was able to judge the body size of others accurately. The findings are discussed in terms of body image distortion specific to oneself in AN. Copyright © 2015 John Wiley & Sons, Ltd and Eating Disorders Association.

  4. How We Experience Being Alone: Age Differences in Affective and Biological Correlates of Momentary Solitude.

    Science.gov (United States)

    Pauly, Theresa; Lay, Jennifer C; Nater, Urs M; Scott, Stacey B; Hoppmann, Christiane A

    2017-01-01

    Spending time alone constitutes a ubiquitous part of our everyday lives. As we get older, alone time increases. Less is known, however, about age differences in the experience of spending time alone (momentary solitude). We examined time-varying associations between momentary solitude, affect quality, and two hypothalamic-pituitary-adrenal axis activity markers [salivary cortisol; dehydroepiandrosterone sulfate (DHEAs)] to better understand the affective and biological correlates of momentary solitude across the adult life span. A total of 185 adults aged 20-81 years (mean age = 49 years, 51% female, 74% Caucasian) completed questionnaires on momentary solitude (alone vs. not alone) and current affect on a handheld device, and provided concurrent saliva samples up to seven times a day for 10 consecutive days. Data were analyzed using multilevel models, controlling for the overall amount of time participants spent alone during the study (overall solitude). Greater overall solitude was associated with decreased average high arousal positive affect and increased average cortisol and DHEAs levels. Momentary solitude was associated with reduced high arousal positive affect, increased low arousal positive affect, and increased low arousal negative affect. Age by momentary solitude interactions indicate that greater age was associated with increased high arousal positive affect and reduced low arousal negative affect during momentary solitude. Furthermore, momentary solitude was associated with increased cortisol and DHEAs. With greater age, the association between momentary solitude and cortisol weakened. Consistent with the negative connotations to loneliness and objective social isolation, greater overall solitude was associated with negative affective and biological correlates. Spending a large overall amount of time alone in old age might thus have negative ramifications for health and well-being. Momentary solitude, in contrast, can be a double-edged sword as

  5. Inelastic neutron scattering experiments with the monochromatic imaging mode of the RITA-II spectrometer

    DEFF Research Database (Denmark)

    Bahl, Christian Robert Haffenden; Lefmann, Kim; Abrahamsen, Asger Bech;

    2006-01-01

    to perform real inelastic neutron scattering experiments. We present the results from inelastic powder, single crystal dispersion and single crystal constant energy mapping experiments. The advantages and complications of performing these experiments are discussed along with a comparison between the imaging...

  6. Cardiac biplane strain imaging: initial in vivo experience.

    NARCIS (Netherlands)

    Lopata, R.G.P.; Nillesen, M.M.; Verrijp, C.N.; Singh, S.K.; Lammens, M.M.Y.; Laak, J.A.W.M. van der; Wetten, H.B. van; Thijssen, J.M.; Kapusta, L.; Korte, C.L. de

    2010-01-01

    In this study, first we propose a biplane strain imaging method using a commercial ultrasound system, yielding estimation of the strain in three orthogonal directions. Secondly, an animal model of a child's heart was introduced that is suitable to simulate congenital heart disease and was used to

  7. Three-tesla imaging of the knee: initial experience

    Energy Technology Data Exchange (ETDEWEB)

    Craig, Joseph G.; Blechinger, Joseph; Hearshen, David; Bouffard, J. Antonio; Diamond, Mark; Holsbeeck, Marnix T. van [Henry Ford Hospital, Department of Diagnostic Radiology, Detroit, MI (United States); Go, Lily [Wayne State University School of Medicine, Detroit, MI (United States)

    2005-08-01

    To assess 3-T imaging of the knee. We reviewed 357 3-T magnetic resonance images of the knee obtained using a dedicated knee coil. From 58 patients who had arthroscopy we determined the sensitivity and specificity for anterior cruciate ligament (ACL) tear and medial and lateral meniscal tear. A chemical shift artifact showed prominently at 3 T even after improvements had been made by increasing the bandwidth. For complete ACL tear the sensitivity was 100% (95% confidence interval, CI, 75.30-100.00), and the specificity was 97.9% (95% CI 87.7-99.9). For the medial meniscus the sensitivity was 100.00% (95% CI 90.0-100.00), and the specificity was 83.3%(95% CI 66.6-95.3). For the lateral meniscus the sensitivity was 66.7% (95% CI 38.4-88.2), and the specificity was 97.6% (95% CI 87.1-99.9). In general 3-T imaging allows a favorable display of anatomy and pathology. The lateral meniscus was assessed to be weaker than the other anatomic structures. Three-tesla imaging allows increased signal-to-noise ratio, increased resolution, and faster scanning times. (orig.)

  8. TRAUMA (RE-)IMAG(IN)ED: EXPERIENCES AND MEMORIES OF ...

    African Journals Online (AJOL)

    imitch

    terms what trauma is, and interfaces it with how Soyinka has (re-)imag(in)ed it and submits ... innermost and visceral thoughts and being of his characters. .... Like The Man Died, Madmen and Specialists arose from Soyinka's painful and traumatic acquaintance ... out of the period, which I stayed in prison, which was just over.

  9. Problems in obtaining perfect images by single-particle electron cryomicroscopy of biological structures in amorphous ice

    OpenAIRE

    Henderson, Richard; McMullan, Greg

    2013-01-01

    Theoretical considerations together with simulations of single-particle electron cryomicroscopy images of biological assemblies in ice demonstrate that atomic structures should be obtainable from images of a few thousand asymmetric units, provided the molecular weight of the whole assembly being studied is greater than the minimum needed for accurate position and orientation determination. However, with present methods of specimen preparation and current microscope and detector...

  10. Biological stress reactivity as an index of the two polarities of the experience model.

    Science.gov (United States)

    Silva, Jaime R; Vivanco-Carlevari, Anastassia; Barrientos, Mauricio; Martínez, Claudio; Salazar, Luis A; Krause, Mariane

    2017-10-01

    The two-polarities model of personality argues that experience is organized around two axes: interpersonal relatedness and self-definition. Differential emphasis on one of these poles defines adaptive and pathological experiences, generating anaclitic or introjective tendencies. The anaclitic pattern, on one hand, has been conceptually related with an exaggerated emphasis on interpersonal relatedness. On the other hand, the introjective pattern has been connected to high levels of self-criticism. The aim of this study was to investigate the psychophysiological basis for this relationship. Specifically, we hypothesized that the anaclitic individual should have a higher biological reactivity to stress (BRS), measured by the cortisol concentration in saliva, in an interpersonal stress induction protocol (Trier Social Stress Test). Contrary to what was expected, the results indicated that introjective participants presented a higher BSR than the anaclitic group. Interestingly, in contrast to their higher BSR, the introjective group reported a diminished subjective stress in relation to the average. In the anaclitic group, a tendency that goes in the opposite direction was found. Theoretical implications of these findings were discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA.

    Science.gov (United States)

    Kobayashi, Amane; Sekiguchi, Yuki; Oroguchi, Tomotaka; Okajima, Koji; Fukuda, Asahi; Oide, Mao; Yamamoto, Masaki; Nakasako, Masayoshi

    2016-07-01

    Coherent X-ray diffraction imaging (CXDI) allows internal structures of biological cells and cellular organelles to be analyzed. CXDI experiments have been conducted at 66 K for frozen-hydrated biological specimens at the SPring-8 Angstrom Compact Free-Electron Laser facility (SACLA). In these cryogenic CXDI experiments using X-ray free-electron laser (XFEL) pulses, specimen particles dispersed on thin membranes of specimen disks are transferred into the vacuum chamber of a diffraction apparatus. Because focused single XFEL pulses destroy specimen particles at the atomic level, diffraction patterns are collected through raster scanning the specimen disks to provide fresh specimen particles in the irradiation area. The efficiency of diffraction data collection in cryogenic experiments depends on the quality of the prepared specimens. Here, detailed procedures for preparing frozen-hydrated biological specimens, particularly thin membranes and devices developed in our laboratory, are reported. In addition, the quality of the frozen-hydrated specimens are evaluated by analyzing the characteristics of the collected diffraction patterns. Based on the experimental results, the internal structures of the frozen-hydrated specimens and the future development for efficient diffraction data collection are discussed.

  12. Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA

    Science.gov (United States)

    Kobayashi, Amane; Sekiguchi, Yuki; Oroguchi, Tomotaka; Okajima, Koji; Fukuda, Asahi; Oide, Mao; Yamamoto, Masaki; Nakasako, Masayoshi

    2016-01-01

    Coherent X-ray diffraction imaging (CXDI) allows internal structures of biological cells and cellular organelles to be analyzed. CXDI experiments have been conducted at 66 K for frozen-hydrated biological specimens at the SPring-8 Angstrom Compact Free-Electron Laser facility (SACLA). In these cryogenic CXDI experiments using X-ray free-electron laser (XFEL) pulses, specimen particles dispersed on thin membranes of specimen disks are transferred into the vacuum chamber of a diffraction apparatus. Because focused single XFEL pulses destroy specimen particles at the atomic level, diffraction patterns are collected through raster scanning the specimen disks to provide fresh specimen particles in the irradiation area. The efficiency of diffraction data collection in cryogenic experiments depends on the quality of the prepared specimens. Here, detailed procedures for preparing frozen-hydrated biological specimens, particularly thin membranes and devices developed in our laboratory, are reported. In addition, the quality of the frozen-hydrated specimens are evaluated by analyzing the characteristics of the collected diffraction patterns. Based on the experimental results, the internal structures of the frozen-hydrated specimens and the future development for efficient diffraction data collection are discussed. PMID:27359147

  13. Resolution criteria in double-slit microscopic imaging experiments

    Science.gov (United States)

    You, Shangting; Kuang, Cuifang; Zhang, Baile

    2016-01-01

    Double-slit imaging is widely used for verifying the resolution of high-resolution and super-resolution microscopies. However, due to the fabrication limits, the slit width is generally non-negligible, which can affect the claimed resolution. In this paper we theoretically calculate the electromagnetic field distribution inside and near the metallic double slit using waveguide mode expansion method, and acquire the far-field image by vectorial Fourier optics. We find that the slit width has minimal influence when the illuminating light is polarized parallel to the slits. In this case, the claimed resolution should be based on the center-to-center distance of the double-slit. PMID:27640808

  14. A Conceptual Framework for Organizing Active Learning Experiences in Biology Instruction

    Science.gov (United States)

    Gardner, Joel; Belland, Brian R.

    2012-08-01

    Introductory biology courses form a cornerstone of undergraduate instruction. However, the predominantly used lecture approach fails to produce higher-order biology learning. Research shows that active learning strategies can increase student learning, yet few biology instructors use all identified active learning strategies. In this paper, we present a framework to design biology instruction that incorporates all active learning strategies. We review active learning research in undergraduate biology courses, present a framework for organizing active learning strategies, and provide clear implications and future research for designing instruction in introductory undergraduate biology courses.

  15. Design Analysis of a Space Based Chromotomographic Hyperspectral Imaging Experiment

    Science.gov (United States)

    2010-03-01

    utilized rather than a refractive lens telescopes for several reasons [26]: • Mirrors do not introduce any chromatic aberration • Mirrors provide a... aberration , but coma and astigmatism are inherent [35]. Mirrors will not cause chromatic aberration , unlike lenses [21]. A field stop is also being used...on a 20 micron pixel pitch. Image Quality: Two times diffration-limited performance or better. Zero chromatic aberration . The collimated beam

  16. Experiments on the use of CCD's to detect photoelectron images

    Science.gov (United States)

    Choisser, J. P.

    1975-01-01

    Image tube design and processing requirements for building an ICCD are discussed. Work is under way at EVC for building an ICCD using the Fairchild CCD 201 (100 x 100) array, and progress will be reported. Demountable tests have been made, exposing parts of a CCD 201 to 15 kilovolt electrons over five radiation levels from approximately 10 to 1 million rads. Other tubes built by EVC over the last few years which successfully use semiconductors to detect photoelectrons will be described briefly.

  17. Design and analysis of experiments with high throughput biological assay data.

    Science.gov (United States)

    Rocke, David M

    2004-12-01

    The design and analysis of experiments using gene expression microarrays is a topic of considerable current research, and work is beginning to appear on the analysis of proteomics and metabolomics data by mass spectrometry and NMR spectroscopy. The literature in this area is evolving rapidly, and commercial software for analysis of array or proteomics data is rarely up to date, and is essentially nonexistent for metabolomics data. In this paper, I review some of the issues that should concern any biologists planning to use such high-throughput biological assay data in an experimental investigation. Technical details are kept to a minimum, and may be found in the referenced literature, as well as in the many excellent papers which space limitations prevent my describing. There are usually a number of viable options for design and analysis of such experiments, but unfortunately, there are even more non-viable ones that have been used even in the published literature. This is an area in which up-to-date knowledge of the literature is indispensable for efficient and effective design and analysis of these experiments. In general, we concentrate on relatively simple analyses, often focusing on identifying differentially expressed genes and the comparable issues in mass spectrometry and NMR spectroscopy (consistent differences in peak heights or areas for example). Complex multivariate and pattern recognition methods also need much attention, but the issues we describe in this paper must be dealt with first. The literature on analysis of proteomics and metabolomics data is as yet sparse, so the main focus of this paper will be on methods devised for analysis of gene expression data that generalize to proteomics and metabolomics, with some specific comments near the end on analysis of metabolomics data by mass spectrometry and NMR spectroscopy.

  18. Micro-Imagers for Spaceborne Cell-Growth Experiments

    Science.gov (United States)

    Behar, Alberto; Matthews, Janet; SaintAnge, Beverly; Tanabe, Helen

    2006-01-01

    A document discusses selected aspects of a continuing effort to develop five micro-imagers for both still and video monitoring of cell cultures to be grown aboard the International Space Station. The approach taken in this effort is to modify and augment pre-existing electronic micro-cameras. Each such camera includes an image-detector integrated-circuit chip, signal-conditioning and image-compression circuitry, and connections for receiving power from, and exchanging data with, external electronic equipment. Four white and four multicolor light-emitting diodes are to be added to each camera for illuminating the specimens to be monitored. The lens used in the original version of each camera is to be replaced with a shorter-focal-length, more-compact singlet lens to make it possible to fit the camera into the limited space allocated to it. Initially, the lenses in the five cameras are to have different focal lengths: the focal lengths are to be 1, 1.5, 2, 2.5, and 3 cm. Once one of the focal lengths is determined to be the most nearly optimum, the remaining four cameras are to be fitted with lenses of that focal length.

  19. Chest wall tuberculosis - A clinical and imaging experience

    Directory of Open Access Journals (Sweden)

    Shabnam Bhandari Grover

    2011-01-01

    Full Text Available Aims: Tuberculous infection of the thoracic cage is rare and is difficult to discern clinically or on radiographs. This study aims to describe the common sites and the imaging appearances of chest wall tuberculosis. Materials and Methods: A retrospective review of the clinical and imaging records of 12 confirmed cases of thoracic cage tuberculosis (excluding that of the spine, seen over the last 7 years, was performed. Imaging studies available included radiographs, ultrasonographies (USGs, and computed tomography (CT scans. Pathological confirmation was obtained in all cases. Results: All patients had clinical signs and symptoms localized to the site of involvement, whether it was the sternum, sternoclavicular joints, or ribs. CT scan revealed sternal destruction in three patients and osteolytic lesions with sclerosis of the articular surfaces of the sternoclavicular joints in two patients. In five patients with rib lesions, USG elegantly demonstrated the bone destruction underlying the cold abscess. All cases were confirmed to be of tuberculous origin by pathology studies of the aspirated/curetted material, obtained by CT / USG guidance. Conclusions: Tuberculous etiology should be considered for patients presenting with atypical sites of skeletal inflammation. CT scan plays an important role in the evaluation of these patients. However, the use of USG for demonstrating rib destruction in a chest wall cold abscess has so far been under-emphasized, as has been the role of CT and USG guided aspiration in confirming the aetiology.

  20. Superoxide-dependent consumption of nitric oxide in biological media may confound in vitro experiments.

    Science.gov (United States)

    Keynes, Robert G; Griffiths, Charmaine; Garthwaite, John

    2003-01-15

    NO functions ubiquitously as a biological messenger but has also been implicated in various pathologies, a role supported by many reports that exogenous or endogenous NO can kill cells in tissue culture. In the course of experiments aimed at examining the toxicity of exogenous NO towards cultured cells, we found that most of the NO delivered using a NONOate (diazeniumdiolate) donor was removed by reaction with the tissue-culture medium. Two NO-consuming ingredients were identified: Hepes buffer and, under laboratory lighting, the vitamin riboflavin. In each case, the loss of NO was reversed by the addition of superoxide dismutase. The effect of Hepes was observed over a range of NONOate concentrations (producing up to 1 microM NO). Furthermore, from measurements of soluble guanylate cyclase activity, Hepes-dependent NO consumption remained significant at the low nanomolar NO concentrations relevant to physiological NO signalling. The combination of Hepes and riboflavin (in the light) acted synergistically to the extent that, instead of a steady-state concentration of about 1 microM being generated, NO was undetectable (<10 nM). Again, the consumption could be inhibited by superoxide dismutase. A scheme is proposed whereby a "vicious cycle" of superoxide radical (O(2)(.-)) formation occurs as a result of oxidation of Hepes to its radical species, fuelled by the subsequent reaction of O(2)(.-) with NO to form peroxynitrite (ONOO(-)). The inadvertent production of ONOO(-) and other reactive species in biological media, or the associated loss of NO, may contribute to the adverse effects, or otherwise, of NO in vitro.

  1. Electrical conductivity imaging of lower extremities using MREIT: postmortem swine and in vivo human experiments.

    Science.gov (United States)

    Woo, Eung Je; Kim, Hyung Joong; Minhas, Atul S; Kim, Young Tae; Jeong, Woo Chul; Kwon, O

    2008-01-01

    Cross-sectional conductivity images of lower extremities were reconstructed using Magnetic Resonance Electrical Impedance Tomography (MREIT) techniques. Carbon-hydrogel electrodes were adopted for postmortem swine and in vivo human imaging experiments. Due to their large surface areas and good contacts on the skin, we could inject as much as 10 mA into the lower extremities of human subjects without producing a painful sensation. Using a 3T MREIT system, we first performed a series of postmortem swine experiments and produced high-resolution conductivity images of swine legs. Validating the experimental protocol for the lower extremities, we revised it for the following human experiments. After the review of the Institutional Review Board (IRB), we conducted our first MREIT experiments of human subjects using the same 3T MREIT system. Collecting magnetic flux density data inside lower extremities subject to multiple injection currents, we reconstructed cross-sectional conductivity images using the harmonic B(z) algorithm. The conductivity images very well distinguished different parts of muscles inside the lower extremities. The outermost fatty layer was clearly shown in each conductivity image. We could observe severe noise in the outer layer of the bones primarily due to the MR signal void phenomenon there. Reconstructed conductivity images indicated that the internal regions of the bones have relatively high conductivity values. Future study is desired in terms of the conductivity image reconstruction algorithm to improve the image quality. Further human imaging experiments are planned and being conducted to produce high-resolution conductivity images from different parts of the human body.

  2. High-resolution MR imaging of periarterial edema associated with biological inflammation in spontaneous carotid dissection

    Energy Technology Data Exchange (ETDEWEB)

    Naggara, Olivier; Marsico, Rodolpho; Meder, Jean-Francois; Oppenheim, Catherine [Paris-Descartes University, Department of Neuroradiology, Paris (France); Touze, Emmanuel; Mas, Jean-Louis [Paris-Descartes University, Department of Neurology, Paris (France); Leclerc, Xavier; Pruvo, Jean-Pierre [University Hospital Roger Salengro, Department of Neuroradiology, Lille (France); Nguyen, Thanh [Boston University Medical Center, Department of Neurology, Neurosurgery, and Radiology, Boston, MA (United States)

    2009-09-15

    It has been suggested that spontaneous cervical carotid artery dissection (sCAD) may result from arterial inflammation. Periarterial edema (PAE), occasionally described in the vicinity of the mural hematoma in patients with sCAD, may support this hypothesis. Using cervical high-resolution magnetic resonance imaging, three readers, blinded to the mechanism of carotid artery dissection, searched for PAE, defined as periarterial T2-hyperintensity and T1-hypointensity, in 29 consecutive CAD patients categorized as spontaneous CAD (sCAD, n = 18) or traumatic CAD (tCAD, n = 11; i.e., major head or neck trauma within 2 weeks before the clinical onset). The relationships between PAE, inflammatory biological markers, history of infection and CAD mechanism were explored. Multiple CADs (n = 8) were found only in sCAD patients. Compared with tCAD, patients with sCAD were more likely to have a recent history of infection (OR = 12.5 [{sub 95%}CI = 1.3-119], p = 0.03), PAE (83% vs. 27%; OR = 13.3 [{sub 95%}CI = 2.2-82.0], p = 0.005) and to have elevated CRP (OR = 6.1 [{sub 95%}CI = 1.2-32.1], p = 0.0002) or ESR (OR = 8.8 [{sub 95%}CI = 1.5-50.1], p = 0.002) values. Interobserver agreement was 0.84 or higher for PAE identification. sCAD was associated with PAE and biological inflammation. Our results support the hypothesis of an underlying arterial inflammation in sCAD. (orig.)

  3. Cardiac biplane strain imaging: initial in vivo experience

    Energy Technology Data Exchange (ETDEWEB)

    Lopata, R G P; Nillesen, M M; Thijssen, J M; De Korte, C L [Clinical Physics Laboratory, Radboud University Nijmegen Medical Centre, Nijmegen (Netherlands); Verrijp, C N; Lammens, M M Y; Van der Laak, J A W M [Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen (Netherlands); Singh, S K; Van Wetten, H B [Department of Cardiothoracic Surgery, Radboud University Nijmegen Medical Centre, Nijmegen (Netherlands); Kapusta, L [Pediatric Cardiology, Department of Pediatrics, Radboud University Nijmegen Medical Centre, Nijmegen (Netherlands)], E-mail: R.Lopata@cukz.umcn.nl

    2010-02-21

    In this study, first we propose a biplane strain imaging method using a commercial ultrasound system, yielding estimation of the strain in three orthogonal directions. Secondly, an animal model of a child's heart was introduced that is suitable to simulate congenital heart disease and was used to test the method in vivo. The proposed approach can serve as a framework to monitor the development of cardiac hypertrophy and fibrosis. A 2D strain estimation technique using radio frequency (RF) ultrasound data was applied. Biplane image acquisition was performed at a relatively low frame rate (<100 Hz) using a commercial platform with an RF interface. For testing the method in vivo, biplane image sequences of the heart were recorded during the cardiac cycle in four dogs with an aortic stenosis. Initial results reveal the feasibility of measuring large radial, circumferential and longitudinal cumulative strain (up to 70%) at a frame rate of 100 Hz. Mean radial strain curves of a manually segmented region-of-interest in the infero-lateral wall show excellent correlation between the measured strain curves acquired in two perpendicular planes. Furthermore, the results show the feasibility and reproducibility of assessing radial, circumferential and longitudinal strains simultaneously. In this preliminary study, three beagles developed an elevated pressure gradient over the aortic valve ({delta}p: 100-200 mmHg) and myocardial hypertrophy. One dog did not develop any sign of hypertrophy ({delta}p = 20 mmHg). Initial strain (rate) results showed that the maximum strain (rate) decreased with increasing valvular stenosis (-50%), which is in accordance with previous studies. Histological findings corroborated these results and showed an increase in fibrotic tissue for the hearts with larger pressure gradients (100, 200 mmHg), as well as lower strain and strain rate values.

  4. Ring imaging Cherenkov detector of PHENIX experiment at RHIC

    CERN Document Server

    Akiba, Y; Burward-Hoy, J; Chappell, R; Crook, D; Ebisu, K; Emery, M S; Ferriera, J; Frawley, A D; Hamagaki, H; Hara, H; Hayano, R S; Hemmick, T K; Hibino, M; Hutter, R; Kennedy, M; Kikuchi, J; Matsumoto, T; Moscone, C G; Nagasaka, Y; Nishimura, S; Oyama, K; Sakaguchi, T; Salomone, S; Shigaki, K; Tanaka, Y; Walker, J W; Wintenberg, A L; Young, G R

    1999-01-01

    The RICH detector of the PHENIX experiment at RHIC is currently under construction. Its main function is to identity electron tracks in a very high particle density, about 1000 charged particles per unit rapidity, expected in the most violent collisions at RHIC. The design and construction status of the detector and its expected performance are described.

  5. Image Schemas in Verb-Particle Constructions: Evidence from a Behavioral Experiment

    Science.gov (United States)

    Yang, Tangfeng

    2016-01-01

    Cognitive linguists claim that verb-particle constructions are compositional and analyzable, and that the particles contribute to the overall meaning in the form of image schemas. This article examined this claim with a behavioral experiment, in which participants were asked to judge the sensibility of short sentences primed by image-schematic…

  6. A Conceptual Framework for Organizing Active Learning Experiences in Biology Instruction

    Science.gov (United States)

    Gardner, Joel; Belland, Brian R.

    2012-01-01

    Introductory biology courses form a cornerstone of undergraduate instruction. However, the predominantly used lecture approach fails to produce higher-order biology learning. Research shows that active learning strategies can increase student learning, yet few biology instructors use all identified active learning strategies. In this paper, we…

  7. A Conceptual Framework for Organizing Active Learning Experiences in Biology Instruction

    Science.gov (United States)

    Gardner, Joel; Belland, Brian R.

    2012-01-01

    Introductory biology courses form a cornerstone of undergraduate instruction. However, the predominantly used lecture approach fails to produce higher-order biology learning. Research shows that active learning strategies can increase student learning, yet few biology instructors use all identified active learning strategies. In this paper, we…

  8. Diffusion and association processes in biological systems: theory, computation and experiment

    Directory of Open Access Journals (Sweden)

    Mereghetti Paolo

    2011-03-01

    Full Text Available Abstract Macromolecular diffusion plays a fundamental role in biological processes. Here, we give an overview of recent methodological advances and some of the challenges for understanding how molecular diffusional properties influence biological function that were highlighted at a recent workshop, BDBDB2, the second Biological Diffusion and Brownian Dynamics Brainstorm.

  9. Diffusion and association processes in biological systems: theory, computation and experiment.

    Science.gov (United States)

    Mereghetti, Paolo; Kokh, Daria; McCammon, J Andrew; Wade, Rebecca C

    2011-03-02

    Macromolecular diffusion plays a fundamental role in biological processes. Here, we give an overview of recent methodological advances and some of the challenges for understanding how molecular diffusional properties influence biological function that were highlighted at a recent workshop, BDBDB2, the second Biological Diffusion and Brownian Dynamics Brainstorm.

  10. Time-resolved diffuse optical tomographic imaging for the provision of both anatomical and functional information about biological tissue

    Science.gov (United States)

    Zhao, Huijuan; Gao, Feng; Tanikawa, Yukari; Homma, Kazuhiro; Yamada, Yukio

    2005-04-01

    We present in vivo images of near-infrared (NIR) diffuse optical tomography (DOT) of human lower legs and forearm to validate the dual functions of a time-resolved (TR) NIR DOT in clinical diagnosis, i.e., to provide anatomical and functional information simultaneously. The NIR DOT system is composed of time-correlated single-photon-counting channels, and the image reconstruction algorithm is based on the modified generalized pulsed spectral technique, which effectively incorporates the TR data with reasonable computation time. The reconstructed scattering images of both the lower legs and the forearm revealed their anatomies, in which the bones were clearly distinguished from the muscles. In the absorption images, some of the blood vessels were observable. In the functional imaging, a subject was requested to do handgripping exercise to stimulate physiological changes in the forearm tissue. The images of oxyhemoglobin, deoxyhemoglobin, and total hemoglobin concentration changes in the forearm were obtained from the differential images of the absorption at three wavelengths between the exercise and the rest states, which were reconstructed with a differential imaging scheme. These images showed increases in both blood volume and oxyhemoglobin concentration in the arteries and simultaneously showed hypoxia in the corresponding muscles. All the results have demonstrated the capability of TR NIR DOT by reconstruction of the absolute images of the scattering and the absorption with a high spatial resolution that finally provided both the anatomical and functional information inside bulky biological tissues.

  11. A qualitative exploration of body image experiences of women progressing through pregnancy.

    Science.gov (United States)

    Watson, Brittany; Broadbent, Jaclyn; Skouteris, Helen; Fuller-Tyszkiewicz, Matthew

    2016-02-01

    Pregnancy provides an interesting challenge to body image theories in that the natural physiological changes push women further from the socioculturally prescribed thin ideal which these theories hinge upon. The impact that these significant physiological changes have on the woman's body image during pregnancy may depend on the extent to which they retain or revise the ideal. However, little is known about body image experiences during pregnancy. To provide a comprehensive exploration of the body image experiences of pregnant women. Individual structured interviews were conducted with 19 currently pregnant women. Transcriptions were analysed using a thematic content analysis approach. Themes extracted from the qualitative data included: (1) women's body image experiences during pregnancy were complex and changing, and shaped by the salience of specific body parts, the women's expectations for future changes to their body within the perinatal period, the functionality of the body, and their experience of maternity clothing, (2) women were able to negotiate the changes to their bodies as they recognised the functionality of the pregnant body, (3) women were surprised by the public nature of the pregnant body, (4) partner support and positive feedback about the pregnant body was highly valued, and (5) the importance of open communication around weight and body image in antenatal healthcare. Our findings highlight the need for the adaptation and expansion of existing body image theories to be used as a framework for women's experiences of pregnancy. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  12. Human cell structure-driven model construction for predicting protein subcellular location from biological images.

    Science.gov (United States)

    Shao, Wei; Liu, Mingxia; Zhang, Daoqiang

    2016-01-01

    The systematic study of subcellular location pattern is very important for fully characterizing the human proteome. Nowadays, with the great advances in automated microscopic imaging, accurate bioimage-based classification methods to predict protein subcellular locations are highly desired. All existing models were constructed on the independent parallel hypothesis, where the cellular component classes are positioned independently in a multi-class classification engine. The important structural information of cellular compartments is missed. To deal with this problem for developing more accurate models, we proposed a novel cell structure-driven classifier construction approach (SC-PSorter) by employing the prior biological structural information in the learning model. Specifically, the structural relationship among the cellular components is reflected by a new codeword matrix under the error correcting output coding framework. Then, we construct multiple SC-PSorter-based classifiers corresponding to the columns of the error correcting output coding codeword matrix using a multi-kernel support vector machine classification approach. Finally, we perform the classifier ensemble by combining those multiple SC-PSorter-based classifiers via majority voting. We evaluate our method on a collection of 1636 immunohistochemistry images from the Human Protein Atlas database. The experimental results show that our method achieves an overall accuracy of 89.0%, which is 6.4% higher than the state-of-the-art method. The dataset and code can be downloaded from https://github.com/shaoweinuaa/. dqzhang@nuaa.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. Thermal Imaging of Forest Canopy Temperatures: Relationships with Biological and Biophysical Drivers and Ecosystem Fluxes

    Science.gov (United States)

    Still, C. J.; Kim, Y.; Hanson, C. V.; Law, B. E.; Kwon, H.; Schulze, M.; Pau, S.; Detto, M.

    2015-12-01

    Temperature is a primary environmental control on plant processes at a range of spatial and temporal scales, affecting enzymatic reactions, ecosystem biogeochemistry, and species distributions. Although most focus is on air temperature, the radiative or skin temperature of plants is more relevant. Canopy skin temperature dynamics reflect biophysical, physiological, and anatomical characteristics and interactions with environmental drivers, and can be used to examine forest responses to stresses like droughts and heat waves. Direct measurements of plant canopy temperatures using thermocouple sensors have been challenging and offer limited information. Such measurements are usually conducted over short periods of time and a limited spatial extent of the canopy. By contrast, thermal infrared (TIR) imaging allows for extensive temporal and spatial measurement of canopy temperature regimes. We present results of TIR imaging of forest canopies at a range of well-studied forest sites in the United States and Panama. These forest types include temperate rainforests, a semi­arid pine forest, and a semi­deciduous tropical forest. Canopy temperature regimes at these sites are highly variable spatially and temporally and display frequent departures from air temperature, particularly during clear sky conditions. Canopy tissue temperatures are often warmer (daytime) and colder (nighttime) than air temperature, and canopy structure seems to have a large influence on the thermal regime. Additionally, comparison of canopy temperatures to eddy covariance fluxes of carbon dioxide, water vapor, and energy reveals relationships not apparent using air temperature. Initial comparisons between our forest canopy temperatures and remotely sensed skin temperature using Landsat and MODIS data show reasonably good agreement. We conclude that temporal and spatial changes in canopy temperature and its relationship to biological and environmental factors can improve our understanding of how

  14. Laser desorption/ionization mass spectrometry for direct profiling and imaging of small molecules from raw biological materials

    Energy Technology Data Exchange (ETDEWEB)

    Cha, Sangwon [Iowa State Univ., Ames, IA (United States)

    2008-01-01

    Matrix-assisted laser desorption/ionization(MALDI) mass spectrometry(MS) has been widely used for analysis of biological molecules, especially macromolecules such as proteins. However, MALDI MS has a problem in small molecule (less than 1 kDa) analysis because of the signal saturation by organic matrixes in the low mass region. In imaging MS (IMS), inhomogeneous surface formation due to the co-crystallization process by organic MALDI matrixes limits the spatial resolution of the mass spectral image. Therefore, to make laser desorption/ionization (LDI) MS more suitable for mass spectral profiling and imaging of small molecules directly from raw biological tissues, LDI MS protocols with various alternative assisting materials were developed and applied to many biological systems of interest. Colloidal graphite was used as a matrix for IMS of small molecules for the first time and methodologies for analyses of small metabolites in rat brain tissues, fruits, and plant tissues were developed. With rat brain tissues, the signal enhancement for cerebroside species by colloidal graphite was observed and images of cerebrosides were successfully generated by IMS. In addition, separation of isobaric lipid ions was performed by imaging tandem MS. Directly from Arabidopsis flowers, flavonoids were successfully profiled and heterogeneous distribution of flavonoids in petals was observed for the first time by graphite-assisted LDI(GALDI) IMS.

  15. Biological Experiments in Microgravity Conditions Using Magnetic Micro- and Nano-Particles

    Science.gov (United States)

    Nechitailo, Galina S.; Kuznetsov, Anatoli; Kuznetsov, Oleg

    2016-07-01

    even for weak magnetic objects, and can have significant effects on multiple processes in living cells/organisms. It was reported, that such high gradient magnetic fields can affect cell differentiation and cell proliferation processes in ground-based experiments. To prevent oxidation of ultradisperse ferromagnetic particles in aqueous media, it is beneficial to coat their surface with carbon. Suitable protected metallic micro- and nano-particles can be produced by a variety of techniques (CVD, plasmachemistry, joint grinding, etc.). Ferro-carbon particles produced by plasmachemical technique have high sorption capacities for various organic and inorganic compounds (as well as for various cell metabolites), can be formed in rather stable aqueous suspensions, and be controlled (e.g., sedimented) by a magnetic field. This makes these particles a very interesting research tool. In our opinion, biological experiments with ferro-carbon nano-structured particles in microgravity will generate important scientific data and will allow creating new methods of negating the adverse effects of microgravity on living systems.

  16. Ames Coronagraph Experiment: Enabling Missions to Directly Image Exoplanets

    Science.gov (United States)

    Belikov, Ruslan

    2014-01-01

    Technology to find biomarkers and life on other worlds is rapidly maturing. If there is a habitable planet around the nearest star, we may be able to detect it this decade with a small satellite mission. In the 2030 decade, we will likely know if there is life in our Galactic neighborhood (1000 nearest stars). The Ames Coronagraph Experiment is developing coronagraphic technologies to enable such missions.

  17. Cosmic AntiParticle Ring Imaging Cerenkov Experiment

    CERN Multimedia

    2002-01-01

    %RE2A \\\\ \\\\ %title \\\\ \\\\The CAPRICE experiment studies antimatter and light nuclei in the cosmic rays as well as muons in the atmosphere. The experiment is performed with the spectrometer shown in the figure which is lifted by a balloon to an altitude of 35-40 km. At this altitude less than half a percent of the atmosphere is above the 2 ton spectrometer which makes it possible to study the cosmic ray flux without too much background from atmospherically produced particles. The spectrometer includes time-of-flight scintillators, a gaseous RICH counter, a drift chamber tracker and a silicon electromagnetic calorimeter. The important feature of the spectrometer is to discriminate between different particles.\\\\ \\\\ The experiment aims at measuring the flux of the antiparticles (antiprotons and positrons) above about 5 GeV and relate the fluxes to models including exotic production of antiparticles like dark matter supersymmetric particles. The flux of muons is measured during descent of the balloon through the at...

  18. Unsupervised biomedical named entity recognition: experiments with clinical and biological texts.

    Science.gov (United States)

    Zhang, Shaodian; Elhadad, Noémie

    2013-12-01

    Named entity recognition is a crucial component of biomedical natural language processing, enabling information extraction and ultimately reasoning over and knowledge discovery from text. Much progress has been made in the design of rule-based and supervised tools, but they are often genre and task dependent. As such, adapting them to different genres of text or identifying new types of entities requires major effort in re-annotation or rule development. In this paper, we propose an unsupervised approach to extracting named entities from biomedical text. We describe a stepwise solution to tackle the challenges of entity boundary detection and entity type classification without relying on any handcrafted rules, heuristics, or annotated data. A noun phrase chunker followed by a filter based on inverse document frequency extracts candidate entities from free text. Classification of candidate entities into categories of interest is carried out by leveraging principles from distributional semantics. Experiments show that our system, especially the entity classification step, yields competitive results on two popular biomedical datasets of clinical notes and biological literature, and outperforms a baseline dictionary match approach. Detailed error analysis provides a road map for future work.

  19. Unsupervised Biomedical Named Entity Recognition: Experiments with Clinical and Biological Texts

    Science.gov (United States)

    Zhang, Shaodian; Elhadad, Nóemie

    2013-01-01

    Named entity recognition is a crucial component of biomedical natural language processing, enabling information extraction and ultimately reasoning over and knowledge discovery from text. Much progress has been made in the design of rule-based and supervised tools, but they are often genre and task dependent. As such, adapting them to different genres of text or identifying new types of entities requires major effort in re-annotation or rule development. In this paper, we propose an unsupervised approach to extracting named entities from biomedical text. We describe a stepwise solution to tackle the challenges of entity boundary detection and entity type classification without relying on any handcrafted rules, heuristics, or annotated data. A noun phrase chunker followed by a filter based on inverse document frequency extracts candidate entities from free text. Classification of candidate entities into categories of interest is carried out by leveraging principles from distributional semantics. Experiments show that our system, especially the entity classification step, yields competitive results on two popular biomedical datasets of clinical notes and biological literature, and outperforms a baseline dictionary match approach. Detailed error analysis provides a road map for future work. PMID:23954592

  20. Stable non-covalent labeling of layered silicate nanoparticles for biological imaging.

    Science.gov (United States)

    Mortimer, Gysell M; Jack, Kevin S; Musumeci, Anthony W; Martin, Darren J; Minchin, Rodney F

    2016-04-01

    Layered silicate nanoparticles (LSN) are widely used in industrial applications and consumer products. They also have potential benefits in biomedical applications such as implantable devices and for drug delivery. To study how nanomaterials interact with cells and tissues, techniques to track and quantify their movement through different biological compartments are essential. While radiolabels can be very sensitive, particularly for in vivo studies, fluorescent labeling has been preferred in recent years because of the array of methods available to image and quantify fluorescent nanoparticles. However, labeling can be problematic, especially if it alters the physical properties of the nanomaterial. Herein is described a novel non-covalent labeling technique for LSN using readily available fluorescent dimeric cyanine dyes without the need to use excess amounts of dye to achieve labeling, or the need for removal of unbound dye. The approach utilizes the cationic binding properties of layered silicate clays and the multiple quaternary nitrogens associated with the dyes. Preparation of YOYO-1 labeled LSN with optimal dispersion in aqueous media is presented. The utilization of the labeled particles is then demonstrated in cell binding and uptake studies using flow cytometry and confocal microscopy. The labeled LSN are highly fluorescent, stable and exhibit identical physical properties with respect to the unlabeled nanoparticles. The general approach described here is applicable to other cyanine dyes and may be utilized more widely for labeling nanoparticles that comprise a crystalline plate structure with a high binding capacity.

  1. Biological effects and physical safety aspects of NMR imaging and in vivo spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tenforde, T.S.; Budinger, T.F.

    1985-08-01

    An assessment is made of the biological effects and physical hazards of static and time-varying fields associated with the NMR devices that are being used for clinical imaging and in vivo spectroscopy. A summary is given of the current state of knowledge concerning the mechanisms of interaction and the bioeffects of these fields. Additional topics that are discussed include: (1) physical effects on pacemakers and metallic implants such as aneurysm clips, (2) human health studies related to the effects of exposure to nonionizing electromagnetic radiation, and (3) extant guidelines for limiting exposure of patients and medical personnel to the fields produced by NMR devices. On the basis of information available at the present time, it is concluded that the fields associated with the current generation of NMR devices do not pose a significant health risk in themselves. However, rigorous guidelines must be followed to avoid the physical interaction of these fields with metallic implants and medical electronic devices. 476 refs., 5 figs., 2 tabs.

  2. Development of instrumentation for routine ToF-SIMS imaging analysis of biological material

    Science.gov (United States)

    Cliff, B.; Lockyer, N. P.; Corlett, C.; Vickerman, J. C.

    2003-01-01

    The routine analysis of frozen-hydrated biological material is a goal that is highly sought after in the ToF-SIMS community. To this end we have developed a system based on an existing protocol developed elsewhere, but with several crucial advances. Here we report on the major design initiatives, some early performance characteristics and experimental data obtained. The system was designed with ease-of-use and reliability in mind in addition to performance, this should make the results repeatable. The device works on a freeze-fracture type method to expose pristine surface for SIMS analysis. An important performance characteristic that has emerged is one of time; the fracture stage can be cooled down to operating temperature within 30 min beginning of cooling. This is important as it minimises dead time at the beginning of an experimental session. We also present here images of freeze-fractured liposomes obtained with this hardware, showing two differing fracture regimes, we believe they are of similar quality to those obtained using other techniques.

  3. Cardiac biplane strain imaging: initial in vivo experience

    Science.gov (United States)

    Lopata, R. G. P.; Nillesen, M. M.; Verrijp, C. N.; Singh, S. K.; Lammens, M. M. Y.; van der Laak, J. A. W. M.; van Wetten, H. B.; Thijssen, J. M.; Kapusta, L.; de Korte, C. L.

    2010-02-01

    In this study, first we propose a biplane strain imaging method using a commercial ultrasound system, yielding estimation of the strain in three orthogonal directions. Secondly, an animal model of a child's heart was introduced that is suitable to simulate congenital heart disease and was used to test the method in vivo. The proposed approach can serve as a framework to monitor the development of cardiac hypertrophy and fibrosis. A 2D strain estimation technique using radio frequency (RF) ultrasound data was applied. Biplane image acquisition was performed at a relatively low frame rate (cardiac cycle in four dogs with an aortic stenosis. Initial results reveal the feasibility of measuring large radial, circumferential and longitudinal cumulative strain (up to 70%) at a frame rate of 100 Hz. Mean radial strain curves of a manually segmented region-of-interest in the infero-lateral wall show excellent correlation between the measured strain curves acquired in two perpendicular planes. Furthermore, the results show the feasibility and reproducibility of assessing radial, circumferential and longitudinal strains simultaneously. In this preliminary study, three beagles developed an elevated pressure gradient over the aortic valve (Δp: 100-200 mmHg) and myocardial hypertrophy. One dog did not develop any sign of hypertrophy (Δp = 20 mmHg). Initial strain (rate) results showed that the maximum strain (rate) decreased with increasing valvular stenosis (-50%), which is in accordance with previous studies. Histological findings corroborated these results and showed an increase in fibrotic tissue for the hearts with larger pressure gradients (100, 200 mmHg), as well as lower strain and strain rate values.

  4. Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy.

    Science.gov (United States)

    Takayama, Yuki; Yonekura, Koji

    2016-03-01

    Coherent X-ray diffraction imaging at cryogenic temperature (cryo-CXDI) allows the analysis of internal structures of unstained, non-crystalline, whole biological samples in micrometre to sub-micrometre dimensions. Targets include cells and cell organelles. This approach involves preparing frozen-hydrated samples under controlled humidity, transferring the samples to a cryo-stage inside a vacuum chamber of a diffractometer, and then exposing the samples to coherent X-rays. Since 2012, cryo-coherent diffraction imaging (CDI) experiments have been carried out with the X-ray free-electron laser (XFEL) at the SPring-8 Ångstrom Compact free-electron LAser (SACLA) facility in Japan. Complementary use of cryo-electron microscopy and/or light microscopy is highly beneficial for both pre-checking samples and studying the integrity or nature of the sample. This article reports the authors' experience in cryo-XFEL-CDI of biological cells and organelles at SACLA, and describes an attempt towards reliable and higher-resolution reconstructions, including signal enhancement with strong scatterers and Patterson-search phasing.

  5. A comprehensive experiment for molecular biology: Determination of single nucleotide polymorphism in human REV3 gene using PCR-RFLP.

    Science.gov (United States)

    Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

    2017-07-08

    Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of DNA polymerase ζ and SNPs in this gene are associated with altered susceptibility to cancer. This newly designed experiment is composed of three parts, including genomic DNA extraction, gene amplification by PCR, and genotyping by RFLP. By combining these activities, the students are not only able to learn a series of biotechniques in molecular biology, but also acquire the ability to link the learned knowledge with practical applications. This comprehensive experiment will help the medical students improve the conceptual understanding of SNP and the technical understanding of SNP detection. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):299-304, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  6. Phase-coded multi-pulse technique for ultrasonic high-order harmonic imaging of biological tissues in vitro.

    Science.gov (United States)

    Ma, Qingyu; Zhang, Dong; Gong, Xiufen; Ma, Yong

    2007-04-07

    Second or higher order harmonic imaging shows significant improvement in image clarity but is degraded by low signal-noise ratio (SNR) compared with fundamental imaging. This paper presents a phase-coded multi-pulse technique to provide the enhancement of SNR for the desired high-order harmonic ultrasonic imaging. In this technique, with N phase-coded pulses excitation, the received Nth harmonic signal is enhanced by 20 log(10)N dB compared with that in the single-pulse mode, whereas the fundamental and other order harmonic components are efficiently suppressed to reduce image confusion. The principle of this technique is theoretically discussed based on the theory of the finite amplitude sound waves, and examined by measurements of the axial and lateral beam profiles as well as the phase shift of the harmonics. In the experimental imaging for two biological tissue specimens, a plane piston source at 2 MHz is used to transmit a sequence of multiple pulses with equidistant phase shift. The second to fifth harmonic images are obtained using this technique with N = 2 to 5, and compared with the images obtained at the fundamental frequency. Results demonstrate that this technique of relying on higher order harmonics seems to provide a better resolution and contrast of ultrasonic images.

  7. Body Image in a Sexual Context : The Relationship between Body Image and Sexual Experiences

    NARCIS (Netherlands)

    van den Brink, F.

    2017-01-01

    Given the large sociocultural emphasis on appearance and the widespread incidence of a negative body image in current society, scientific understanding of its potential psychological and physical health consequences, including sexual problems, is now of particular importance. The value of

  8. Experiences of the foster care process in the Republic of Ireland: retrospective accounts from biological children of foster carers

    OpenAIRE

    Williams, David

    2014-01-01

    This thesis examines the experiences of the biological children of foster carers. In particular it explores their experiences in relation to inclusion, consultation and decision-making. The study also examines the support and training needs of birth children in foster families. Using a qualitative methodology in-depth, semi-structured interviews were conducted with fifteen birth children of foster carers aged between 18 and 30 years. The research findings show that for the majority of birth c...

  9. The analysis of frequency domain characteristics of emotional images in eye-tracking experiment

    Science.gov (United States)

    Fan, Boqiang; Ma, Huimin; Wang, Xiang

    2015-07-01

    Although recently eye-tracking method has been introduced into behavioral experiments based on dot-probe paradigm, some characteristics in eye-tracking data do not draw as much attention as traditional characteristics like reaction time. It is also necessary to associate eye-tracking data to characteristics of images shown in experiments. In this research, new variables, such as fixation length, times of fixation and times of eye movement, in eye-tracking data were extracted from a behavioral experiment based on dot probe paradigm. They were analyzed and compared to traditional reaction time. After the analysis of positive and negative scenery images, parameters such as hue frequency spectrum PAR (Peak to Average Ratio) were extracted and showed difference between negative and positive images. These parameters of emotional images could discriminate scenery images according to their emotions in an SVM classifier well. Besides, it was found that images' hue frequency spectrum PAR is obviously relevant to eye-tracking statistics. When the dot was on the negative side, negative images' hue frequency spectrum PAR and horizontal eye-jumps confirmed to hyperbolic distribution, while that of positive images was linear with horizontal eye-jumps. The result could help to explain the mechanism of human's attention and boost the study in computer vision.

  10. Object-based attentional modulation of biological motion processing: spatiotemporal dynamics using functional magnetic resonance imaging and electroencephalography.

    Science.gov (United States)

    Safford, Ashley S; Hussey, Elizabeth A; Parasuraman, Raja; Thompson, James C

    2010-07-07

    Although it is well documented that the ability to perceive biological motion is mediated by the lateral temporal cortex, whether and when neural activity in this brain region is modulated by attention is unknown. In particular, it is unclear whether the processing of biological motion requires attention or whether such stimuli are processed preattentively. Here, we used functional magnetic resonance imaging, high-density electroencephalography, and cortically constrained source estimation methods to investigate the spatiotemporal effects of attention on the processing of biological motion. Directing attention to tool motion in overlapping movies of biological motion and tool motion suppressed the blood oxygenation level-dependent (BOLD) response of the right superior temporal sulcus (STS)/middle temporal gyrus (MTG), while directing attention to biological motion suppressed the BOLD response of the left inferior temporal sulcus (ITS)/MTG. Similarly, category-based modulation of the cortical current source density estimates from the right STS/MTG and left ITS was observed beginning at approximately 450 ms following stimulus onset. Our results indicate that the cortical processing of biological motion is strongly modulated by attention. These findings argue against preattentive processing of biological motion in the presence of stimuli that compete for attention. Our findings also suggest that the attention-based segregation of motion category-specific responses only emerges relatively late (several hundred milliseconds) in processing.

  11. MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME

    Science.gov (United States)

    Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

    2017-01-01

    Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments. PMID:28190948

  12. The relationship study between image features and detection probability based on psychology experiments

    Science.gov (United States)

    Lin, Wei; Chen, Yu-hua; Wang, Ji-yuan; Gao, Hong-sheng; Wang, Ji-jun; Su, Rong-hua; Mao, Wei

    2011-04-01

    Detection probability is an important index to represent and estimate target viability, which provides basis for target recognition and decision-making. But it will expend a mass of time and manpower to obtain detection probability in reality. At the same time, due to the different interpretation of personnel practice knowledge and experience, a great difference will often exist in the datum obtained. By means of studying the relationship between image features and perception quantity based on psychology experiments, the probability model has been established, in which the process is as following.Firstly, four image features have been extracted and quantified, which affect directly detection. Four feature similarity degrees between target and background were defined. Secondly, the relationship between single image feature similarity degree and perception quantity was set up based on psychological principle, and psychological experiments of target interpretation were designed which includes about five hundred people for interpretation and two hundred images. In order to reduce image features correlativity, a lot of artificial synthesis images have been made which include images with single brightness feature difference, images with single chromaticity feature difference, images with single texture feature difference and images with single shape feature difference. By analyzing and fitting a mass of experiments datum, the model quantitys have been determined. Finally, by applying statistical decision theory and experimental results, the relationship between perception quantity with target detection probability has been found. With the verification of a great deal of target interpretation in practice, the target detection probability can be obtained by the model quickly and objectively.

  13. Transforming Misconceptions: Using Transformative Experience to Promote Positive Affect and Conceptual Change in Students Learning about Biological Evolution

    Science.gov (United States)

    Heddy, Benjamin C.; Sinatra, Gale M.

    2013-01-01

    Teaching and learning about complex scientific content, such as biological evolution, is challenging in part because students have a difficult time seeing the relevance of evolution in their everyday lives. The purpose of this study was to explore the effectiveness of the Teaching for Transformative Experiences in Science (TTES) model (Pugh, 2002)…

  14. Effects of an Educational Experience Incorporating an Inventory of Factors Potentially Influencing Student Acceptance of Biological Evolution

    Science.gov (United States)

    Wiles, Jason R.; Alters, Brian

    2011-01-01

    This investigation provides an extensive review of scientific, religious, and otherwise non-scientific factors that may influence student acceptance of biological evolution. We also measure the extent to which students' levels of acceptance changed following an educational experience designed to address an inclusive inventory of factors identified…

  15. Transforming Misconceptions: Using Transformative Experience to Promote Positive Affect and Conceptual Change in Students Learning about Biological Evolution

    Science.gov (United States)

    Heddy, Benjamin C.; Sinatra, Gale M.

    2013-01-01

    Teaching and learning about complex scientific content, such as biological evolution, is challenging in part because students have a difficult time seeing the relevance of evolution in their everyday lives. The purpose of this study was to explore the effectiveness of the Teaching for Transformative Experiences in Science (TTES) model (Pugh, 2002)…

  16. More Ideas for Monitoring Biological Experiments with the BBC Computer: Absorption Spectra, Yeast Growth, Enzyme Reactions and Animal Behaviour.

    Science.gov (United States)

    Openshaw, Peter

    1988-01-01

    Presented are five ideas for A-level biology experiments using a laboratory computer interface. Topics investigated include photosynthesis, yeast growth, animal movements, pulse rates, and oxygen consumption and production by organisms. Includes instructions specific to the BBC computer system. (CW)

  17. A unique large-scale undergraduate research experience in molecular systems biology for non-mathematics majors.

    Science.gov (United States)

    Kappler, Ulrike; Rowland, Susan L; Pedwell, Rhianna K

    2016-12-28

    Systems biology is frequently taught with an emphasis on mathematical modeling approaches. This focus effectively excludes most biology, biochemistry, and molecular biology students, who are not mathematics majors. The mathematical focus can also present a misleading picture of systems biology, which is a multi-disciplinary pursuit requiring collaboration between biochemists, bioinformaticians, and mathematicians. This article describes an authentic large-scale undergraduate research experience (ALURE) in systems biology that incorporates proteomics, bacterial genomics, and bioinformatics in the one exercise. This project is designed to engage students who have a basic grounding in protein chemistry and metabolism and no mathematical modeling skills. The pedagogy around the research experience is designed to help students attack complex datasets and use their emergent metabolic knowledge to make meaning from large amounts of raw data. On completing the ALURE, participants reported a significant increase in their confidence around analyzing large datasets, while the majority of the cohort reported good or great gains in a variety of skills including "analysing data for patterns" and "conducting database or internet searches." An environmental scan shows that this ALURE is the only undergraduate-level system-biology research project offered on a large-scale in Australia; this speaks to the perceived difficulty of implementing such an opportunity for students. We argue however, that based on the student feedback, allowing undergraduate students to complete a systems-biology project is both feasible and desirable, even if the students are not maths and computing majors. © 2016 by The International Union of Biochemistry and Molecular Biology, 2016.

  18. Thermal Design, Test and Analysis of PharmaSat, a Small Class D Spacecraft with a Biological Experiment

    Science.gov (United States)

    Diaz-Aguado, Millan F.; VanOutryve, Cassandra; Ghassemiah, Shakib; Beasley, Christopher; Schooley, Aaron

    2009-01-01

    Small spacecraft have been increasing in popularity because of their low cost, short turnaround and relative efficiency. In the past, small spacecraft have been primarily used for technology demonstrations, but advances in technology have made the miniaturization of space science possible [1,2]. PharmaSat is a low cost, small three cube size spacecraft, with a biological experiment on board, built at NASA (National Aeronautics and Space Administration) Ames Research Center. The thermal design of small spacecraft presents challenges as their smaller surface areas translate into power and thermal constraints. The spacecraft is thermally designed to run colder in the Low Earth Orbit space environment, and heated to reach the temperatures required by the science payload. The limited power supply obtained from the solar panels on small surfaces creates a constraint in the power used to heat the payload to required temperatures. The pressurized payload is isolated with low thermally conductance paths from the large ambient temperature changes. The thermal design consists of different optical properties of section surfaces, Multi Layer Insulation (MLI), low thermal conductance materials, flexible heaters and thermal spreaders. The payload temperature is controlled with temperature sensors and flexible heaters. Finite Element Analysis (FEA) and testing were used to aid the thermal design of the spacecraft. Various tests were conducted to verify the thermal design. An infrared imager was used on the electronic boards to find large heat sources and eliminate any possible temperature runaways. The spacecraft was tested in a thermal vacuum chamber to optimize the thermal and power analysis and qualify the thermal design of the spacecraft for the mission.

  19. Thermal Design, Test and Analysis of PharmaSat, a Small Class D Spacecraft with a Biological Experiment

    Science.gov (United States)

    Diaz-Aguado, Millan F.; VanOutryve, Cassandra; Ghassemiah, Shakib; Beasley, Christopher; Schooley, Aaron

    2009-01-01

    Small spacecraft have been increasing in popularity because of their low cost, short turnaround and relative efficiency. In the past, small spacecraft have been primarily used for technology demonstrations, but advances in technology have made the miniaturization of space science possible [1,2]. PharmaSat is a low cost, small three cube size spacecraft, with a biological experiment on board, built at NASA (National Aeronautics and Space Administration) Ames Research Center. The thermal design of small spacecraft presents challenges as their smaller surface areas translate into power and thermal constraints. The spacecraft is thermally designed to run colder in the Low Earth Orbit space environment, and heated to reach the temperatures required by the science payload. The limited power supply obtained from the solar panels on small surfaces creates a constraint in the power used to heat the payload to required temperatures. The pressurized payload is isolated with low thermally conductance paths from the large ambient temperature changes. The thermal design consists of different optical properties of section surfaces, Multi Layer Insulation (MLI), low thermal conductance materials, flexible heaters and thermal spreaders. The payload temperature is controlled with temperature sensors and flexible heaters. Finite Element Analysis (FEA) and testing were used to aid the thermal design of the spacecraft. Various tests were conducted to verify the thermal design. An infrared imager was used on the electronic boards to find large heat sources and eliminate any possible temperature runaways. The spacecraft was tested in a thermal vacuum chamber to optimize the thermal and power analysis and qualify the thermal design of the spacecraft for the mission.

  20. Experience – Information – Image: A Historiography of Unfolding. Arab Cinema as Example

    Directory of Open Access Journals (Sweden)

    Laura U. Marks

    2011-04-01

    Full Text Available Why do certain images of history reach us, while others remain seemingly forgotten, in the infinite breadth of the past? Why do only certain events seem to matter? I suggest those experiences are not forgotten but enfolded. The contemporary politics of historiography can be conceptualized according to the relationship between Experience, Information, and Image; a triadic relationship I have proposed to understand the nature of the image in the information age. While Experience is infinite, the vast majority of experience lies latent. Few Images ever arise from it. In our age, those that do tend to be selected, or unfolded, by political and economic interests that deem them to be useful as Information. Nevertheless, anyone can unfold any aspect of Experience to become a public image, and artists (and others do so in order to allow other aspects of Experience to circulate, before they enfold, back into the matrix of history. I will show an animated diagram that illustrates this concept of history as a flow of unfolding and enfolding, influenced by concepts from Charles Sanders Peirce and Gilles Deleuze.   Many artworks can be illuminated by this process. My examples will be drawn from contemporary Arab cinema. In the heavily politicized Arab milieu, the Image world is constructed as a selective unfolding of only those aspects of Experience that are deemed to be useful or profitable. Some Arab filmmakers, rather than deconstruct the resulting ideological images, prefer to carry out their own unfoldings:  explicating hitherto latent events, knowledges, and sensations. Thus what official history deems merely personal, absurd, micro-events, or no events at all, becomes the stuff of a rich alternative historiography. This process characterizes the work of, among others, Joana Hadjithomas and Khalil Joreige, Nisrine Khodr, Mohammed Soueid, and Akram Zaatari (Lebanon, Azza El-Hassan, Elia Suleiman, and Sobhi Al-Zobaidi (Palestine, and Mohamad Khan

  1. Fetal magnetic resonance imaging: jumping from 1.5 to 3 tesla (preliminary experience)

    Energy Technology Data Exchange (ETDEWEB)

    Victoria, Teresa [The Children' s Hospital of Philadelphia, Radiology Department, Center for Fetal Diagnosis and Treatment, Philadelphia, PA (United States); Jaramillo, Diego; Roberts, Timothy Paul Leslie; Zarnow, Deborah; Johnson, Ann Michelle; Delgado, Jorge; Vossough, Arastoo [The Children' s Hospital of Philadelphia, Radiology Department, Philadelphia, PA (United States); Rubesova, Erika [Stanford University, Department of Radiology, Lucile Packard Children' s Hospital, Stanford, CA (United States)

    2014-04-15

    Several attempts have been made at imaging the fetus at 3 T as part of the continuous search for increased image signal and better anatomical delineation of the developing fetus. Until very recently, imaging of the fetus at 3 T has been disappointing, with numerous artifacts impeding image analysis. Better magnets and coils and improved technology now allow imaging of the fetus at greater magnetic strength, some hurdles in the shape of imaging artifacts notwithstanding. In this paper we present the preliminary experience of evaluating the developing fetus at 3 T and discuss several artifacts encountered and techniques to decrease them, as well as safety concerns associated with scanning the fetus at higher magnetic strength. (orig.)

  2. Robust overlay schemes for the fusion of fluorescence and color channels in biological imaging.

    Science.gov (United States)

    Glatz, Jürgen; Symvoulidis, Panagiotis; Garcia-Allende, P Beatriz; Ntziachristos, Vasilis

    2014-04-01

    Molecular fluorescence imaging is a commonly used method in various biomedical fields and is undergoing rapid translation toward clinical applications. Color images are commonly superimposed with fluorescence measurements to provide orientation, anatomical information, and molecular tissue properties in a single image. New adaptive methods that produce a more robust composite image than conventional lime green alpha blending are presented and demonstrated herein. Moreover, visualization through temporal changes is showcased as an alternative for real-time imaging systems.

  3. TOPICAL REVIEW: Single-molecule experiments in biological physics: methods and applications

    Science.gov (United States)

    Ritort, F.

    2006-08-01

    I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.

  4. Identifying genes relevant to specific biological conditions in time course microarray experiments.

    Science.gov (United States)

    Singh, Nitesh Kumar; Repsilber, Dirk; Liebscher, Volkmar; Taher, Leila; Fuellen, Georg

    2013-01-01

    Microarrays have been useful in understanding various biological processes by allowing the simultaneous study of the expression of thousands of genes. However, the analysis of microarray data is a challenging task. One of the key problems in microarray analysis is the classification of unknown expression profiles. Specifically, the often large number of non-informative genes on the microarray adversely affects the performance and efficiency of classification algorithms. Furthermore, the skewed ratio of sample to variable poses a risk of overfitting. Thus, in this context, feature selection methods become crucial to select relevant genes and, hence, improve classification accuracy. In this study, we investigated feature selection methods based on gene expression profiles and protein interactions. We found that in our setup, the addition of protein interaction information did not contribute to any significant improvement of the classification results. Furthermore, we developed a novel feature selection method that relies exclusively on observed gene expression changes in microarray experiments, which we call "relative Signal-to-Noise ratio" (rSNR). More precisely, the rSNR ranks genes based on their specificity to an experimental condition, by comparing intrinsic variation, i.e. variation in gene expression within an experimental condition, with extrinsic variation, i.e. variation in gene expression across experimental conditions. Genes with low variation within an experimental condition of interest and high variation across experimental conditions are ranked higher, and help in improving classification accuracy. We compared different feature selection methods on two time-series microarray datasets and one static microarray dataset. We found that the rSNR performed generally better than the other methods.

  5. Special conference of the American Association for Cancer Research on molecular imaging in cancer: linking biology, function, and clinical applications in vivo.

    Science.gov (United States)

    Luker, Gary D

    2002-04-01

    The AACR Special Conference on Molecular Imaging in Cancer: Linking Biology, Function, and Clinical Applications In Vivo, was held January 23-27, 2002, at the Contemporary Hotel, Walt Disney World, Orlando, FL. Co-Chairs David Piwnica-Worms, Patricia Price and Thomas Meade brought together researchers with diverse expertise in molecular biology, gene therapy, chemistry, engineering, pharmacology, and imaging to accelerate progress in developing and applying technologies for imaging specific cellular and molecular signals in living animals and humans. The format of the conference was the presentation of research that focused on basic and translational biology of cancer and current state-of-the-art techniques for molecular imaging in animal models and humans. This report summarizes the special conference on molecular imaging, highlighting the interfaces of molecular biology with animal models, instrumentation, chemistry, and pharmacology that are essential to convert the dreams and promise of molecular imaging into improved understanding, diagnosis, and management of cancer.

  6. Space Resources for Teachers: Biology, Including Suggestions for Classroom Activities and Laboratory Experiments.

    Science.gov (United States)

    Lee, Tom E.; And Others

    This compilation of resource units concerns the latest developments in space biology. Some of the topics included are oxygen consumption, temperature, radiation, rhythms, weightlessness, acceleration and vibration stress, toxicity, and sensory and perceptual problems. Many of the topics are interdisciplinary and relate biology, physiology,…

  7. Body Image in a Sexual Context : The Relationship between Body Image and Sexual Experiences

    NARCIS (Netherlands)

    van den Brink, F.

    2017-01-01

    Given the large sociocultural emphasis on appearance and the widespread incidence of a negative body image in current society, scientific understanding of its potential psychological and physical health consequences, including sexual problems, is now of particular importance. The value of understand

  8. Exploring the complexities of body image experiences in middle age and older adult women within an exercise context: The simultaneous existence of negative and positive body images.

    Science.gov (United States)

    Bailey, K Alysse; Cline, Lindsay E; Gammage, Kimberley L

    2016-06-01

    Despite many body changes that accompany the aging process, the extant research is limited on middle age and older adults' body image experiences. The purpose of the present study was to explore how body image is represented for middle age and older adult women. Using thematic analysis, 10 women over the age of 55 were interviewed within an exercise context. The following themes were found: body dissatisfaction, body satisfaction despite ageist stereotypes, neutral body image within cohort, and positive body image characteristics. Negative and positive body images were experienced simultaneously, with neutral experiences expressed as low levels of dissatisfaction. This supports the contention that negative and positive body images exist on separate continuums and neutral body image is likely on the same continuum as negative body image. Programs that foster a social support network to reduce negative body image and improve positive body image in older female populations are needed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Multifrequency radar imaging of ash plumes: an experiment at Stromboli

    Science.gov (United States)

    Donnadieu, Franck; Freret-Lorgeril, Valentin; Delanoë, Julien; Vinson, Jean-Paul; Peyrin, Frédéric; Hervier, Claude; Caudoux, Christophe; Van Baelen, Joël; Latchimy, Thierry

    2016-04-01

    Volcanic ash emissions in the atmosphere are hazardous to aviation while ash fallout affects people and human activities and may cause damage to infrastructures and economic losses. In the framework of the French Government Laboratory of Excellence ClerVolc initiative, an experiment was carried out on Stromboli volcano (Italy), between 28 September and 4 October 2015. The aim was to retrieve various physical properties of the ash plumes, especially the mass loading parameters which are critical for the modelling of ash dispersal. We used a complementary set of cutting edge techniques recording in different bands of the electromagnetic spectrum. The innovative instrument setup consisted in three radars, hyperspectral thermal infrared and dual-band UV cameras, a mini DOAS-Flyspec and a multigas sensor. A drone equipped with differential GPS was flown near the ash plumes with several sensors including SO2, CO2 and particle counter. We mainly focus on radar measurements of over 200 ash plumes and present some preliminary comparisons at three frequencies. The BASTA Doppler radar at 95 GHz, originally designed for atmospheric studies, was deployed at about 2.2 km in slant distance from the eruptive craters. It was configured to observe volumes above one of the active craters with a spatio-temporal resolution of 12.5 m and 1 s. From the same location, a 1.2 GHz volcano Doppler radar (VOLDORAD) was recording the signature of ballistics and small lapilli at 0.15 s in 60 m-deep volumes. In addition, a commercial 24 GHz micro rain Doppler radar (MRR) simultaneously recorded activity from the Rochette station, at 400 to 650 m from the active craters with a sampling rate of 10 s and a resolution of 25 m. The latter was pointing almost perpendicularly to the other radar beams. Reflectivity factors were measured inside the ash plume above the source vent by the BASTA radar (3 mm wavelength) spanning -9 to +21 dBZ. Fallout could sometimes be tracked during several minutes within

  10. Easy synthesis of highly fluorescent carbon dots from albumin and their photoluminescent mechanism and biological imaging applications.

    Science.gov (United States)

    Hu, Xiaohua; An, Xueqin; Li, Lielie

    2016-01-01

    A simple and green approach was developed to synthesize highly fluorescent carbon dots (CDs) using albumin as a carbon source in aqueous solution at room temperature. The CDs were characterized by excellent monodispersion, superior photostability, pH-independent emission, long fluorescence lifetime and high quantum yield (QY). The photoluminescent (PL) mechanism of CDs was explored by means of time-resolved PL decay, and the results revealed that PL originated from the emission of both defect state and intrinsic state. In addition, biological imaging with the application of CDs was carried out in human breast cancer Bcap-37 cell, which demonstrated that CDs were provided with an excellent biocompatibility, low cytotoxicity and good transmembrane ability. Besides, CDs could be considered as a potential substitute for organic dyes or semiconductor quantum dots (SQDs) in biological imaging.

  11. Methodological challenges of optical tweezers-based X-ray fluorescence imaging of biological model organisms at synchrotron facilities.

    Science.gov (United States)

    Vergucht, Eva; Brans, Toon; Beunis, Filip; Garrevoet, Jan; Bauters, Stephen; De Rijcke, Maarten; Deruytter, David; Janssen, Colin; Riekel, Christian; Burghammer, Manfred; Vincze, Laszlo

    2015-07-01

    Recently, a radically new synchrotron radiation-based elemental imaging approach for the analysis of biological model organisms and single cells in their natural in vivo state was introduced. The methodology combines optical tweezers (OT) technology for non-contact laser-based sample manipulation with synchrotron radiation confocal X-ray fluorescence (XRF) microimaging for the first time at ESRF-ID13. The optical manipulation possibilities and limitations of biological model organisms, the OT setup developments for XRF imaging and the confocal XRF-related challenges are reported. In general, the applicability of the OT-based setup is extended with the aim of introducing the OT XRF methodology in all research fields where highly sensitive in vivo multi-elemental analysis is of relevance at the (sub)micrometre spatial resolution level.

  12. Structural biology at the single particle level: imaging tobacco mosaic virus by low-energy electron holography

    CERN Document Server

    Longchamp, Jean-Nicolas; Escher, Conrad; Fink, Hans-Werner

    2014-01-01

    Modern structural biology relies on NMR, X-ray crystallography and cryo-electron microscopy for gaining information on biomolecules at nanometer, sub-nanometer or atomic resolution. All these methods, however, require averaging over a vast ensemble of entities and hence knowledge on the conformational landscape of an individual particle is lost. Unfortunately, there are now strong indications that even X-ray free electron lasers will not be able to image individual molecules but will require nanocrystal samples. Here, we show that non-destructive structural biology of single particles has now become possible by means of low-energy electron holography. Individual tobacco mosaic viruses deposited on ultraclean freestanding graphene are imaged at one nanometer resolution revealing structural details arising from the helical arrangement of the outer protein shell of the virus. Since low-energy electron holography is a lens-less technique and since electrons with a deBroglie wavelength of approximately 1 Angstrom ...

  13. Two-Dimensional Standing Wave Total Internal Reflection Fluorescence Microscopy: Superresolution Imaging of Single Molecular and Biological Specimens

    OpenAIRE

    2007-01-01

    The development of high resolution, high speed imaging techniques allows the study of dynamical processes in biological systems. Lateral resolution improvement of up to a factor of 2 has been achieved using structured illumination. In a total internal reflection fluorescence microscope, an evanescence excitation field is formed as light is total internally reflected at an interface between a high and a low index medium. The

  14. VQone MATLAB toolbox: A graphical experiment builder for image and video quality evaluations: VQone MATLAB toolbox.

    Science.gov (United States)

    Nuutinen, Mikko; Virtanen, Toni; Rummukainen, Olli; Häkkinen, Jukka

    2016-03-01

    This article presents VQone, a graphical experiment builder, written as a MATLAB toolbox, developed for image and video quality ratings. VQone contains the main elements needed for the subjective image and video quality rating process. This includes building and conducting experiments and data analysis. All functions can be controlled through graphical user interfaces. The experiment builder includes many standardized image and video quality rating methods. Moreover, it enables the creation of new methods or modified versions from standard methods. VQone is distributed free of charge under the terms of the GNU general public license and allows code modifications to be made so that the program's functions can be adjusted according to a user's requirements. VQone is available for download from the project page (http://www.helsinki.fi/psychology/groups/visualcognition/).

  15. Focal-Plane Imaging of Crossed Beams in Nonlinear Optics Experiments

    Science.gov (United States)

    Bivolaru, Daniel; Herring, G. C.

    2007-01-01

    An application of focal-plane imaging that can be used as a real time diagnostic of beam crossing in various optical techniques is reported. We discuss two specific versions and demonstrate the capability of maximizing system performance with an example in a combined dual-pump coherent anti-Stokes Raman scattering interferometric Rayleigh scattering experiment (CARS-IRS). We find that this imaging diagnostic significantly reduces beam alignment time and loss of CARS-IRS signals due to inadvertent misalignments.

  16. THE ROLE OF LANGUAGE GAME IN THE BUILDING UP OF A POLITICIAN'S IMAGE (PRAGMALINGUISTIC PERLOCUTIONARY EXPERIMENT)

    OpenAIRE

    Khanina E. A.

    2016-01-01

    The article discusses the results of the pragmalinguistic experiment. Since language game is a result of speech creative work, which manifests the individuality of a linguistic personality, the politician can intentionally use language game and thereby consciously form his attractive image. The politician, who uses different kinds of language game, makes some personal characteristics building up the portrait aspect of effective political image more distinguished and thus affects the election ...

  17. Experience in reading digital images may decrease observer accuracy in mammography

    Science.gov (United States)

    Rawashdeh, Mohammad A.; Lewis, Sarah J.; Lee, Warwick; Mello-Thoms, Claudia; Reed, Warren M.; McEntee, Mark; Tapia, Kriscia; Brennan, Patrick C.

    2015-03-01

    Rationale and Objectives: To identify parameters linked to higher levels of performance in screening mammography. In particular we explored whether experience in reading digital cases enhances radiologists' performance. Methods: A total of 60 cases were presented to the readers, of which 20 contained cancers and 40 showed no abnormality. Each case comprised of four images and 129 breast readers participated in the study. Each reader was asked to identify and locate any malignancies using a 1-5 confidence scale. All images were displayed using 5MP monitors, supported by radiology workstations with full image manipulation capabilities. A jack-knife free-response receiver operating characteristic, figure of merit (JAFROC, FOM) methodology was employed to assess reader performance. Details were obtained from each reader regarding their experience, qualifications and breast reading activities. Spearman and Mann Whitney U techniques were used for statistical analysis. Results: Higher performance was positively related to numbers of years professionally qualified (r= 0.18; P<0.05), number of years reading breast images (r= 0.24; P<0.01), number of mammography images read per year (r= 0.28; P<0.001) and number of hours reading mammographic images per week (r= 0.19; P<0.04). Unexpectedly, higher performance was inversely linked to previous experience with digital images (r= - 0.17; p<0.05) and further analysis, demonstrated that this finding was due to changes in specificity. Conclusion: This study suggests suggestion that readers with experience in digital images reporting may exhibit a reduced ability to correctly identify normal appearances requires further investigation. Higher performance is linked to number of cases read per year.

  18. High throughput second harmonic imaging for label-free biological applications

    KAUST Repository

    Macias Romero, Carlos

    2014-01-01

    Second harmonic generation (SHG) is inherently sensitive to the absence of spatial centrosymmetry, which can render it intrinsically sensitive to interfacial processes, chemical changes and electrochemical responses. Here, we seek to improve the imaging throughput of SHG microscopy by using a wide-field imaging scheme in combination with a medium-range repetition rate amplified near infrared femtosecond laser source and gated detection. The imaging throughput of this configuration is tested by measuring the optical image contrast for different image acquisition times of BaTiO3 nanoparticles in two different wide-field setups and one commercial point-scanning configuration. We find that the second harmonic imaging throughput is improved by 2-3 orders of magnitude compared to point-scan imaging. Capitalizing on this result, we perform low fluence imaging of (parts of) living mammalian neurons in culture.

  19. Mapping Chemical and Structural Composition of Pharmaceutical and Biological Samples by Raman, Surface-Enhanced Raman and Fluorescence Spectral Imaging

    Science.gov (United States)

    Chourpa, Igor; Cohen-Jonathan, Simone; Dubois, Pierre

    Raman spectroscopy is an analytical technique recognised for its structural and conformational specificity. The efficient discrimination of molecular species by Raman is particularly potent for multidimensional microscopic imaging of complex biological environment, as demonstrated in the present book. The commonly admitted problem of Raman, low sensitivity, can often be circumvented due to high output instruments and via approaches like RRS (resonance Raman scattering), SERS (surface-enhanced Raman scattering), TERS (tip-enhanced Raman scattering) or CARS (coherent anti-Stokes Raman scattering). In contrast to the latter, RRS and SERS are realizable with less sophisticated set-up based on common Raman systems. Although more invasive than RRS, SERS provides better sensitivity and quenching of fluorescence. SERRS (surface-enhanced resonance Raman scattering) spectroscopy can be used in coupling with fluorescence and competes in selectivity and sensitivity with spectrofluorimetry. In the chapter below, we use recent applications made in our group to illustrate the use of Raman and SERRS spectral imaging for characterization of biological samples (animal subcutaneous tissue, human cancer cells) and pharmaceutical samples (microparticles for drug delivery, fibres for wound dressing). After a brief description of experimental details on spectral imaging, the chapter will focus on results concerning (i) biocompatible pharmaceutical materials made of alginates and (ii) anticancer drugs in pharmaceutical forms and in biological systems.

  20. 3-D surface scan of biological samples with a push-broom imaging spectrometer

    Science.gov (United States)

    The food industry is always on the lookout for sensing technologies for rapid and nondestructive inspection of food products. Hyperspectral imaging technology integrates both imaging and spectroscopy into unique imaging sensors. Its application for food safety and quality inspection has made signifi...

  1. Complete Two-dimensional Muellermetric Imaging of Biological Tissue Using Heterodyned Optical Coherence Tomography

    CERN Document Server

    Liu, Xue; Shahriar, M S

    2010-01-01

    A polarization-sensitive optical coherence tomography system based on heterodyning and filtering techniques is built to perform Stokesmetric imaging of different layers of depths in a porcine tendon sample. The complete 4\\times4 backscattering Muellermetric images of one layer are acquired using such a system. The images reveal information indiscernible from a conventional OCT system.

  2. Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark.

    Science.gov (United States)

    Klein, Max; Sharma, Rati; Bohrer, Chris H; Avelis, Cameron M; Roberts, Elijah

    2017-01-15

    Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology.

  3. Backward Multiscattering and Transport of Photons in Biological Tissue: Experiment and Simulation

    OpenAIRE

    Hamed Mohamed Abubaker; Pavel Tomanek

    2012-01-01

    Optical polarimetry is a mighty tool for study of transparent and translucent inorganic and organic materials. Growing interest in better health and also the quality of the food pointed the investigation of physical properties of biological turbid tissues. Due to the fact that biological tissue is complex random material showing inhomogeneity, anisotropy and nonlinearity in the structure, its rigorous characterization is almost impossible. This complexity also involves an important amount of ...

  4. Space experiment "Cellular Responses to Radiation in Space (CellRad)": Hardware and biological system tests.

    Science.gov (United States)

    Hellweg, Christine E; Dilruba, Shahana; Adrian, Astrid; Feles, Sebastian; Schmitz, Claudia; Berger, Thomas; Przybyla, Bartos; Briganti, Luca; Franz, Markus; Segerer, Jürgen; Spitta, Luis F; Henschenmacher, Bernd; Konda, Bikash; Diegeler, Sebastian; Baumstark-Khan, Christa; Panitz, Corinna; Reitz, Günther

    2015-11-01

    One factor contributing to the high uncertainty in radiation risk assessment for long-term space missions is the insufficient knowledge about possible interactions of radiation with other spaceflight environmental factors. Such factors, e.g. microgravity, have to be considered as possibly additive or even synergistic factors in cancerogenesis. Regarding the effects of microgravity on signal transduction, it cannot be excluded that microgravity alters the cellular response to cosmic radiation, which comprises a complex network of signaling pathways. The purpose of the experiment "Cellular Responses to Radiation in Space" (CellRad, formerly CERASP) is to study the effects of combined exposure to microgravity, radiation and general space flight conditions on mammalian cells, in particular Human Embryonic Kidney (HEK) cells that are stably transfected with different plasmids allowing monitoring of proliferation and the Nuclear Factor κB (NF-κB) pathway by means of fluorescent proteins. The cells will be seeded on ground in multiwell plate units (MPUs), transported to the ISS, and irradiated by an artificial radiation source after an adaptation period at 0 × g and 1 × g. After different incubation periods, the cells will be fixed by pumping a formaldehyde solution into the MPUs. Ground control samples will be treated in the same way. For implementation of CellRad in the Biolab on the International Space Station (ISS), tests of the hardware and the biological systems were performed. The sequence of different steps in MPU fabrication (cutting, drilling, cleaning, growth surface coating, and sterilization) was optimized in order to reach full biocompatibility. Different coatings of the foil used as growth surface revealed that coating with 0.1 mg/ml poly-D-lysine supports cell attachment better than collagen type I. The tests of prototype hardware (Science Model) proved its full functionality for automated medium change, irradiation and fixation of cells. Exposure of

  5. Space experiment "Cellular Responses to Radiation in Space (CELLRAD)": Hardware and biological system tests

    Science.gov (United States)

    Hellweg, Christine E.; Dilruba, Shahana; Adrian, Astrid; Feles, Sebastian; Schmitz, Claudia; Berger, Thomas; Przybyla, Bartos; Briganti, Luca; Franz, Markus; Segerer, Jürgen; Spitta, Luis F.; Henschenmacher, Bernd; Konda, Bikash; Diegeler, Sebastian; Baumstark-Khan, Christa; Panitz, Corinna; Reitz, Günther

    2015-11-01

    One factor contributing to the high uncertainty in radiation risk assessment for long-term space missions is the insufficient knowledge about possible interactions of radiation with other spaceflight environmental factors. Such factors, e.g. microgravity, have to be considered as possibly additive or even synergistic factors in cancerogenesis. Regarding the effects of microgravity on signal transduction, it cannot be excluded that microgravity alters the cellular response to cosmic radiation, which comprises a complex network of signaling pathways. The purpose of the experiment "Cellular Responses to Radiation in Space" (CELLRAD, formerly CERASP) is to study the effects of combined exposure to microgravity, radiation and general space flight conditions on mammalian cells, in particular Human Embryonic Kidney (HEK) cells that are stably transfected with different plasmids allowing monitoring of proliferation and the Nuclear Factor κB (NF-κB) pathway by means of fluorescent proteins. The cells will be seeded on ground in multiwell plate units (MPUs), transported to the ISS, and irradiated by an artificial radiation source after an adaptation period at 0 × g and 1 × g. After different incubation periods, the cells will be fixed by pumping a formaldehyde solution into the MPUs. Ground control samples will be treated in the same way. For implementation of CELLRAD in the Biolab on the International Space Station (ISS), tests of the hardware and the biological systems were performed. The sequence of different steps in MPU fabrication (cutting, drilling, cleaning, growth surface coating, and sterilization) was optimized in order to reach full biocompatibility. Different coatings of the foil used as growth surface revealed that coating with 0.1 mg/ml poly-D-lysine supports cell attachment better than collagen type I. The tests of prototype hardware (Science Model) proved its full functionality for automated medium change, irradiation and fixation of cells. Exposure of

  6. Body image and sexual orientation: The experiences of lesbian and bisexual women.

    Science.gov (United States)

    Smith, Marie L; Telford, Elina; Tree, Jeremy J

    2017-02-01

    Western cultures promote a thin and curvaceous ideal body size that most women find difficult to achieve by healthy measures, resulting in poor body image and increased risk for eating pathology. Research focusing on body image in lesbian and bisexual women has yielded inconsistent results. In total, 11 lesbian and bisexual women were interviewed regarding their experiences with body image. Interpretative phenomenological analysis revealed that these women experienced similar mainstream pressures to conform to a thin body ideal. Furthermore, participants perceived additional pressure to conform to heteronormative standards of beauty since the normalisation of homosexuality and the increase in Lesbian, Gay, Bisexual and Transgender representation in mainstream media.

  7. The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization.

    Science.gov (United States)

    Morrell, William C; Birkel, Garrett W; Forrer, Mark; Lopez, Teresa; Backman, Tyler W H; Dussault, Michael; Petzold, Christopher J; Baidoo, Edward E K; Costello, Zak; Ando, David; Alonso-Gutierrez, Jorge; George, Kevin W; Mukhopadhyay, Aindrila; Vaino, Ian; Keasling, Jay D; Adams, Paul D; Hillson, Nathan J; Garcia Martin, Hector

    2017-09-08

    Although recent advances in synthetic biology allow us to produce biological designs more efficiently than ever, our ability to predict the end result of these designs is still nascent. Predictive models require large amounts of high-quality data to be parametrized and tested, which are not generally available. Here, we present the Experiment Data Depot (EDD), an online tool designed as a repository of experimental data and metadata. EDD provides a convenient way to upload a variety of data types, visualize these data, and export them in a standardized fashion for use with predictive algorithms. In this paper, we describe EDD and showcase its utility for three different use cases: storage of characterized synthetic biology parts, leveraging proteomics data to improve biofuel yield, and the use of extracellular metabolite concentrations to predict intracellular metabolic fluxes.

  8. Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.

    Science.gov (United States)

    Van Valen, David A; Kudo, Takamasa; Lane, Keara M; Macklin, Derek N; Quach, Nicolas T; DeFelice, Mialy M; Maayan, Inbal; Tanouchi, Yu; Ashley, Euan A; Covert, Markus W

    2016-11-01

    Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domains of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.

  9. Programmable Adaptive Spectral Imagers for Mission-Specific Application in Chemical/Biological Sensing

    Science.gov (United States)

    2006-01-01

    detection of chemical/biological agents. Extensive research into both passive remote chemical/biological sensors and active laser- based ( LIDAR ... photodetector (Fig. 1). Fig. 1. Adaptive spectrograph concept: light from a standoff spectral scene is dispersed, dynamically encoded with...the purpose. Data acquisition and processing software was developed for the control of the DMA, capturing data from the photodetectors , and for

  10. Genelab: Scientific Partnerships and an Open-Access Database to Maximize Usage of Omics Data from Space Biology Experiments

    Science.gov (United States)

    Reinsch, S. S.; Galazka, J..; Berrios, D. C; Chakravarty, K.; Fogle, H.; Lai, S.; Bokyo, V.; Timucin, L. R.; Tran, P.; Skidmore, M.

    2016-01-01

    NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. The GeneLab Data System (GLDS) is NASA's premier open-access omics data platform for biological experiments. GLDS houses standards-compliant, high-throughput sequencing and other omics data from spaceflight-relevant experiments. The GeneLab project at NASA-Ames Research Center is developing the database, and also partnering with spaceflight projects through sharing or augmentation of experiment samples to expand omics analyses on precious spaceflight samples. The partnerships ensure that the maximum amount of data is garnered from spaceflight experiments and made publically available as rapidly as possible via the GLDS. GLDS Version 1.0, went online in April 2015. Software updates and new data releases occur at least quarterly. As of October 2016, the GLDS contains 80 datasets and has search and download capabilities. Version 2.0 is slated for release in September of 2017 and will have expanded, integrated search capabilities leveraging other public omics databases (NCBI GEO, PRIDE, MG-RAST). Future versions in this multi-phase project will provide a collaborative platform for omics data analysis. Data from experiments that explore the biological effects of the spaceflight environment on a wide variety of model organisms are housed in the GLDS including data from rodents, invertebrates, plants and microbes. Human datasets are currently limited to those with anonymized data (e.g., from cultured cell lines). GeneLab ensures prompt release and open access to high-throughput genomics, transcriptomics, proteomics, and metabolomics data from spaceflight and ground-based simulations of microgravity, radiation or other space environment factors. The data are meticulously curated to assure that accurate experimental and sample processing metadata are included with each data set. GLDS download volumes indicate strong

  11. Magnetoacoustic tomography with magnetic induction (MAT-MI) for imaging electrical conductivity of biological tissue: a tutorial review

    Science.gov (United States)

    Li, Xu; Yu, Kai; He, Bin

    2016-09-01

    Magnetoacoustic tomography with magnetic induction (MAT-MI) is a noninvasive imaging method developed to map electrical conductivity of biological tissue with millimeter level spatial resolution. In MAT-MI, a time-varying magnetic stimulation is applied to induce eddy current inside the conductive tissue sample. In the presence of a static magnetic field, the Lorentz force acting on the induced eddy current drives mechanical vibrations producing detectable ultrasound signals. These ultrasound signals can then be acquired to reconstruct a map related to the sample’s electrical conductivity contrast. This work reviews fundamental ideas of MAT-MI and major techniques developed in recent years. First, the physical mechanisms underlying MAT-MI imaging are described, including the magnetic induction and Lorentz force induced acoustic wave propagation. Second, experimental setups and various imaging strategies for MAT-MI are reviewed and compared, together with the corresponding experimental results. In addition, as a recently developed reverse mode of MAT-MI, magneto-acousto-electrical tomography with magnetic induction is briefly reviewed in terms of its theory and experimental studies. Finally, we give our opinions on existing challenges and future directions for MAT-MI research. With all the reported and future technical advancement, MAT-MI has the potential to become an important noninvasive modality for electrical conductivity imaging of biological tissue.

  12. Recent developments in widely tunable and high peak power ultrafast laser sources and their adoption in biological imaging

    Science.gov (United States)

    Klein, J.

    2016-03-01

    Widely tunable ultrafast lasers have enabled a large number of biological imaging techniques including point scanning multiphoton excited fluorescence (MPEF), SHG/THG and stimulated Raman imaging. Tunable ultrafast lasers offer spectral agility, covering the entire relative transparency window in live tissue (700-1300nnm) and flexibility with multi-color, synchronized outputs to support sophisticated label free techniques (e.g. stimulated Raman modalities). More recently newly available high peak power lasers based on Ytterbium technology drive advances in two-photon light-sheet, 3 photon excited fluorescence and holographic patterning for optogenetics photo-stimulation. These laser platforms offer a unique blend of compactness, ease of use and cost efficiency, and ideally complement tunable platforms typically based on Ti:Sapphire and IR optical parametric oscillators (OPO). We present various types of ultrafast laser architectures, link their optical characteristics to key bio-imaging requirements, and present relevant examples and images illustrating their impact in biological science. In particular we review the use of ultrafast lasers in optogenetics for photo-stimulation of networks of neurons.

  13. Motion-Corrected Real-Time Cine Magnetic Resonance Imaging of the Heart: Initial Clinical Experience.

    Science.gov (United States)

    Rahsepar, Amir Ali; Saybasili, Haris; Ghasemiesfe, Ahmadreza; Dolan, Ryan S; Shehata, Monda L; Botelho, Marcos P; Markl, Michael; Spottiswoode, Bruce; Collins, Jeremy D; Carr, James C

    2017-08-29

    Free-breathing real-time (RT) imaging can be used in patients with difficulty in breath-holding; however, RT cine imaging typically experiences poor image quality compared with segmented cine imaging because of low resolution. Here, we validate a novel unsupervised motion-corrected (MOCO) reconstruction technique for free-breathing RT cardiac images, called MOCO-RT. Motion-corrected RT uses elastic image registration to generate a single heartbeat of high-quality data from a free-breathing RT acquisition. Segmented balanced steady-state free precession (bSSFP) cine images and free-breathing RT images (Cartesian, TGRAPPA factor 4) were acquired with the same spatial/temporal resolution in 40 patients using clinical 1.5 T magnetic resonance scanners. The respiratory cycle was estimated using the reconstructed RT images, and nonrigid unsupervised motion correction was applied to eliminate breathing motion. Conventional segmented RT and MOCO-RT single-heartbeat cine images were analyzed to evaluate left ventricular (LV) function and volume measurements. Two radiologists scored images for overall image quality, artifact, noise, and wall motion abnormalities. Intraclass correlation coefficient was used to assess the reliability of MOCO-RT measurement. Intraclass correlation coefficient showed excellent reliability (intraclass correlation coefficient ≥ 0.95) of MOCO-RT with segmented cine in measuring LV function, mass, and volume. Comparison of the qualitative ratings indicated comparable image quality for MOCO-RT (4.80 ± 0.35) with segmented cine (4.45 ± 0.88, P = 0.215) and significantly higher than conventional RT techniques (3.51 ± 0.41, P cine (1.51 ± 0.90, P = 0.088 and 1.23 ± 0.45, P = 0.182) were not different. Wall motion abnormality ratings were comparable among different techniques (P = 0.96). The MOCO-RT technique can be used to process conventional free-breathing RT cine images and provides comparable quantitative assessment of LV function and volume

  14. Improving the life science (biology) laboratory education experience: From an instructor-centered to a learner-centered educational environment

    Science.gov (United States)

    Stevens, Marcella Liffick

    The component parts of the educational experience in a freshman biology laboratory course could be improved if the knowledge, skills, and personality of the students could be integrated with the instructor's. Lack of integration of instruction with learning often results in students unwilling or unable to learn content and to transfer it to future courses. This research examined the component parts of instruction and learning for a freshman biology laboratory class and provided an alternative approach to the traditional experience in this lab. Outcome assessment revealed that students experiencing a learner-centered lab responded differently to instruction than students in the traditional lab did and expressed more of a learning orientation and awareness. Not all methods used were successful but course evaluations demonstrated an increased awareness of the learning process among students in the learner-centered lab. The alternative group indicated differences specifically directed toward learning, more often than the traditional group did.

  15. Discrimination methods for biological contaminants in fresh-cut lettuce based on VNIR and NIR hyperspectral imaging

    Science.gov (United States)

    Mo, Changyeun; Kim, Giyoung; Kim, Moon S.; Lim, Jongguk; Lee, Seung Hyun; Lee, Hong-Seok; Cho, Byoung-Kwan

    2017-09-01

    The rapid detection of biological contaminants such as worms in fresh-cut vegetables is necessary to improve the efficiency of visual inspections carried out by workers. Multispectral imaging algorithms were developed using visible-near-infrared (VNIR) and near-infrared (NIR) hyperspectral imaging (HSI) techniques to detect worms in fresh-cut lettuce. The optimal wavebands that can detect worms in fresh-cut lettuce were investigated for each type of HSI using one-way ANOVA. Worm-detection imaging algorithms for VNIR and NIR imaging exhibited prediction accuracies of 97.00% (RI547/945) and 100.0% (RI1064/1176, SI1064-1176, RSI-I(1064-1173)/1064, and RSI-II(1064-1176)/(1064+1176)), respectively. The two HSI techniques revealed that spectral images with a pixel size of 1 × 1 mm or 2 × 2 mm had the best classification accuracy for worms. The results demonstrate that hyperspectral reflectance imaging techniques have the potential to detect worms in fresh-cut lettuce. Future research relating to this work will focus on a real-time sorting system for lettuce that can simultaneously detect various defects such as browning, worms, and slugs.

  16. [Diagnostic image management and communication systems: experience at the University of Pisa].

    Science.gov (United States)

    Caramella, D; Del Sarto, M; Bartolozzi, C; Beltrame, F; Sobel, I

    1995-01-01

    Our work was aimed at implementing and validating a system for the acquisition, local management and remote transmission of diagnostic images. Integration of imaging equipment was performed in each of the two sites (5 km apart) in which the Department of Radiology of the University of Pisa is divided. Teleradiology was carried out using 64 Kbit/s lines as well as a 140 Mbit/s Metropolitan Area Network compliant with the Distributed Queue Dual Bus standard. Application domains included remote expert consultation and teleprocessing of diagnostic images. Remote expert consultation was performed in particular by using the 34 Mbit/s interconnection with the Metropolitan Area Network of Florence. Remote processing of diagnostic images using the high speed link allowed the cooperative work with scientific institutions in a field often limited by the complexity of image transfer and by the lack of a timely feed-back concerning the clinical value of processed images. Advanced processing of diagnostic images was performed in the field of stereographic display of CT and MR data sets. Moreover, experience was gained in the visualization, on a single composite image, of the multiparametric data obtained by means of different MR sequences (T1, Spin Density, T2), thus allowing to summarize, by using false colors, different tissue contrast information.

  17. Status Report for Experiment AD-4/ACE Biological Effectiveness of Antiproton Annihilation

    CERN Document Server

    Holzscheiter, M H; Angelopoulos, Angelo; Bassler, Niels; Beyer, Gerd; Currell, Fred; De Marco, John; Doser, Michael; Hajdukovic, Dragan; Hartley, Oliver; Kavanagh, Joy; Iwamoto, Kei; Jäkel, Oliver; Kantemiris, Ioannis; Knudsen, Helge; Kovacevic, Sandra; McBride, Bill; Møller, Søren Pape; Overgaard, Jens; Petersen, Jørgen; Ratib, Osman; Schettino, Giuseppe; Timson, David; Singers-Sørensen, Brita; Solberg, Timothy; Vranjes, Sanja; Wouters, Brad

    2009-01-01

    Status report for experiment AD-4/ACE showing recent progress in RBE measurements for V79 Chinese Hamster cells irradiated with antiprotons. Also discussed are initial test experiments using the H2AX assay to study DNA damage to cells and initial experiments using liquid ionization chambers.

  18. Development and hydrology of biological soil crusts -- first results from a surface inoculation experiment

    Science.gov (United States)

    Mykhailova, Larysa; Raab, Thomas; Gypser, Stella; Fischer, Thomas

    2016-04-01

    GLA substrate etc. The experiment started at 12.02.2015 and was located at an open area in the vicinity of a meteorological station, where all relevant for HYDRUS modeling data, as well as global radiation have been recorded every 10 min. Crust development was monitored by non-destructive NDVI imaging and a per lysimeter determination of the areal share of biocrust developmental stages: mineral surface (NDVI ≤ 0), BSC1 (0 0.40). The general water balance equation and the amount of lysimeter leachate were used to determine evaporation and changes in water stocks by regular weighing. Biomass growth was inhibited in summer compared to autumn, where mosses developed faster than algae. Finer grained substrate promoted biocrust growth. Evapotranspiration increased with biomass development, presumably because the amount of water held close to the surface increased with biomass. It can be expected that this effect strengthens with increasing amounts of silt and clay. Biodiversity studies are pending, but incipient biocrust growth in the controls points to atmogenic superinfection. So far, it can be concluded that availability of water, depending on both precipitation and substrate texture, were the driving factors of biocrust development. Apart from runoff losses in hillslope conditions, biocrusts are hypothesized to take advantage over their vascular competitors by preventing water infiltration into deeper soil through increased evapotranspiration.

  19. Backward Multiscattering and Transport of Photons in Biological Tissue: Experiment and Simulation

    Directory of Open Access Journals (Sweden)

    Hamed Mohamed Abubaker

    2012-01-01

    Full Text Available Optical polarimetry is a mighty tool for study of transparent and translucent inorganic and organic materials. Growing interest in better health and also the quality of the food pointed the investigation of physical properties of biological turbid tissues. Due to the fact that biological tissue is complex random material showing inhomogeneity, anisotropy and nonlinearity in the structure, its rigorous characterization is almost impossible. This complexity also involves an important amount of information. Therefore, the research of polarization states of scattered light is one of emerging novel techniques in biomedical science. The paper deals with the experimental study of degree of polarization and also with simulation of the biological tissue by Monte Carlo method.

  20. Correlation between iodine-131 MIBG imaging and biological markers in advanced neuroblastoma

    Energy Technology Data Exchange (ETDEWEB)

    Yeh, S.D.; Helson, L.; Benua, R.S.

    1988-01-01

    I-131 metaiodobenzylguanidine (MIBG) imaging was performed in 38 patients with advanced neuroblastoma. Abnormal images were found in patients with elevations of urinary vanillylmandelic acid and dopamine and high serum neuron-specific enolase levels. Normal or minimal elevation of markers was seen in patients with negative images. In follow-up studies after chemotherapy, the disappearance of abnormal uptake was noted in those patients with normal marker values. A persistently abnormal uptake occurred in patients with high marker values. Conversion from a normal image to an abnormal image also occurred in patients whose markers became elevated. I-131 MIBG imaging is sensitive in detecting active foci of a neuroblastoma and is useful in monitoring chemotherapy in these patients.

  1. Classical images as quantum entanglement: An image processing analogy of the GHZ experiment

    Science.gov (United States)

    Goldin, Matías A.; Francisco, Diego; Ledesma, Silvia

    2011-04-01

    In this paper we present an optical analogy of quantum entanglement by means of classical images. As in previous works, the quantum state of two or more qbits is encoded by using the spatial modulation in amplitude and phase of an electromagnetic field. We show here that bidimensional encoding of two qbit states allows us to interpret some non local features of the joint measurement by the assumption of “astigmatic” observers with different resolving power in two orthogonal directions. As an application, we discuss the optical simulation of measuring a system characterized by multiparticle entanglement. The simulation is based on a local representation of entanglement and a classical interferometric system. In particular we show how to simulate the Greenberger-Horne Zeilinger (GHZ) argument and the experimental results which interpretation illustrates the conflict between quantum mechanics and local realism.

  2. Advances in imaging and electron physics time resolved electron diffraction for chemistry, biology and material science

    CERN Document Server

    Hawkes, Peter W

    2014-01-01

    Advances in Imaging & Electron Physics merges two long-running serials-Advances in Electronics & Electron Physics and Advances in Optical & Electron Microscopy. The series features extended articles on the physics of electron devices (especially semiconductor devices), particle optics at high and low energies, microlithography, image science and digital image processing, electromagnetic wave propagation, electron microscopy, and the computing methods used in all these domains. Contributions from leading authorities Informs and updates on all the latest developments in the field.

  3. Indigenous development of an imaging flow cytometer for clinical and biological applications

    Science.gov (United States)

    J, Veerendra Kalyan; Srinivasan, Rajesh; Gorthi, Sai Siva

    2014-10-01

    Flow cytometry is a benchmark technique used for basic research and clinical diagnosis of various diseases. Despite being a high-throughput technique, it fails in capturing the morphology of cells being analyzed. Imaging flow cytometry is a combination of flow-cytometry and digital microscopy, which offers advantages of both the techniques. In this paper, we report on the development of an indigenous Imaging Flow Cytometer, realized with the combination of Optics, Microfluidics, and High-speed imaging. A custom-made bright-field transmission microscope is used to capture images of cells flowing across the microfluidic device. High-throughput morphological analysis on suspension of yeast cells is presented.

  4. Spatially resolved, diffuse reflectance imaging for subsurface pattern visualization toward development of a lensless imaging platform: phantom experiments

    Science.gov (United States)

    Schelkanova, Irina; Pandya, Aditya; Saiko, Guennadi; Nacy, Lidia; Babar, Hannan; Shah, Duoaud; Lilge, Lothar; Douplik, Alexandre

    2016-01-01

    A portable, spatially resolved, diffuse reflectance lensless imaging technique based on the charge-coupled device or complementary metal-oxide semiconductor sensor directly coupled to the fiber optic bundle is proposed for visualization of subsurface structures such as superficial microvasculature in the epithelium. We discuss an experimental method for emulating a lensless imaging setup via raster scanning a single fiber-optic cable over a microfluidic phantom containing periodic hemoglobin absorption contrast. To evaluate the ability of the technique to recover information about the subsurface linear structures, scattering layers formed of the Sylgard® 184 Silicone Elastomer and titanium dioxide were placed atop the microfluidic phantom. Thickness of the layers ranged from 0.2 to 0.7 mm, and the values of the reduced scattering coefficient (μs‧) were between 0.85 and 4.25 mm-1. The results demonstrate that fiber-optic, lensless platform can be used for two-dimensional imaging of absorbing inclusions in diffuse reflectance mode. In these experiments, it was shown that diffuse reflectance imaging can provide sufficient spatial sampling of the phantom for differentiation of 30 μm structural features of the embedded absorbing pattern inside the scattering media.

  5. Transrectal ultrasonography and magnetic resonance imaging in the staging of rectal cancer. Effect of experience

    DEFF Research Database (Denmark)

    Rafaelsen, Søren R; Sørensen, Torben; Jakobsen, Anders

    2008-01-01

    OBJECTIVE: To evaluate the effect of experience on preoperative staging of rectal cancer using magnetic resonance imaging (MRI) and transrectal ultrasound (TRUS). MATERIAL AND METHODS: From January 2002 to May 2006, 134 consecutive patients with biopsy-proven rectal cancer were examined with a 1....... In addition to this supervision, the person responsible for staging should be trained through a defined training programme....

  6. Particle imaging velocimetry experiments and lattice-Boltzmann simulations on a single sphere settling under gravity

    NARCIS (Netherlands)

    Ten Cate, A.; Nieuwstad, C.H.; Derksen, J.J.; Van den Akker, H.E.A.

    2002-01-01

    A comparison is made between experiments and simulations on a single sphere settling in silicon oil in a box. Cross-correlation particle imaging velocimetry measurements were carried out at particle Reynolds numbers ranging from 1.5 to 31.9. The particle Stokes number varied from 0.2 to 4 and at bot

  7. In situ single molecule imaging of cell membranes: linking basic nanotechniques to cell biology, immunology and medicine.

    Science.gov (United States)

    Pi, Jiang; Jin, Hua; Yang, Fen; Chen, Zheng W; Cai, Jiye

    2014-11-01

    The cell membrane, which consists of a viscous phospholipid bilayer, different kinds of proteins and various nano/micrometer-sized domains, plays a very important role in ensuring the stability of the intracellular environment and the order of cellular signal transductions. Exploring the precise cell membrane structure and detailed functions of the biomolecules in a cell membrane would be helpful to understand the underlying mechanisms involved in cell membrane signal transductions, which could further benefit research into cell biology, immunology and medicine. The detection of membrane biomolecules at the single molecule level can provide some subtle information about the molecular structure and the functions of the cell membrane. In particular, information obtained about the molecular mechanisms and other information at the single molecule level are significantly different from that detected from a large amount of biomolecules at the large-scale through traditional techniques, and can thus provide a novel perspective for the study of cell membrane structures and functions. However, the precise investigations of membrane biomolecules prompts researchers to explore cell membranes at the single molecule level by the use of in situ imaging methods, as the exact conformation and functions of biomolecules are highly controlled by the native cellular environment. Recently, the in situ single molecule imaging of cell membranes has attracted increasing attention from cell biologists and immunologists. The size of biomolecules and their clusters on the cell surface are set at the nanoscale, which makes it mandatory to use high- and super-resolution imaging techniques to realize the in situ single molecule imaging of cell membranes. In the past few decades, some amazing imaging techniques and instruments with super resolution have been widely developed for molecule imaging, which can also be further employed for the in situ single molecule imaging of cell membranes. In

  8. Ten Years' Experience with an E-Learning Lecture Series on Cancer Biology and Pharmacology

    Science.gov (United States)

    Efferth, Thomas

    2013-01-01

    In life sciences, the internet is an indispensable medium for research, but has not yet realized its full potential for teaching. The concept of e-learning has been developed over the past decades for undergraduate, graduate and postgraduate programs. We set up an e-learning lecture on cancer biology and pharmacology that was first offered in 2003…

  9. Infusing Bioinformatics and Research-Like Experience into a Molecular Biology Laboratory Course

    Science.gov (United States)

    Nogaj, Luiza A.

    2014-01-01

    A nine-week laboratory project designed for a sophomore level molecular biology course is described. Small groups of students (3-4 per group) choose a tumor suppressor gene (TSG) or an oncogene for this project. Each group researches the role of their TSG/oncogene from primary literature articles and uses bioinformatics engines to find the gene…

  10. Variability of Biological Degradation of Phenolic Hydrocarbons in an Aerobic Aquifer Determined by Laboratory Batch Experiments

    DEFF Research Database (Denmark)

    Nielsen, Per Henning; Christensen, Thomas Højlund

    1994-01-01

    The biological aerobic degradation of 7 phenolic hydrocarbons (phenol, o-cresol, o-nitrophenol, p-nitrophenol, 2,6-dichlorophenol, 2,4-dichlorophenol, 4,6-o-dichlorocresol) and 1 aromatic hydrocarbon (nitrobenzene) was studied for 149 days in replicate laboratory batch microcosms with sediment...

  11. An Experiment of the Malkus-Lorenz Waterwheel and Its Measurement by Image Processing

    Science.gov (United States)

    Kim, Heewon; Seo, Jiwon; Jeong, Bora; Min, Chohong

    We introduce a simple and efficient experimental setup for the Malkus-Lorenz waterwheel. Through a series of image processing techniques, our work is listed as one of the few experiments that measure not only the angular velocity but also the mass distribution. Our experiment is to observe qualitative changes on the waterwheel as the leakage rate changes, while the other physical parameters are fixed. We perform a bifurcation analysis for the qualitative changes, and the phase portraits from experiments are validated by the bifurcation analysis.

  12. The Role of Imagery and Experiences in the Construction of a Tourism Destination Image

    Directory of Open Access Journals (Sweden)

    Nelson Matos

    2015-06-01

    Full Text Available This paper addresses the role of imagery and tourism experiences (TEs in the construction of tourism destination image (TDI. It highlights the importance of the construct imagery at all stages of consumption, because of the intangibility that characterizes tourism and services in general. This aspect gains importance since it is impossible for tourists to experience the desired holidays prior to visitation, leading the way for imagery to become an essential element to inspire and to influence them during the decision-making process, and consumption before, during and after the experience. A conceptual model resulting from the literature review and the potential theoretical contribution of the model are discussed.

  13. Case studies in quantitative biology: Biochemistry on a leash and a single-molecule Hershey-Chase experiment

    Science.gov (United States)

    Van Valen, David

    2011-12-01

    The last 50 years of biological research has seen a marked increase in the amount of quantitative data that describes living systems. This wealth of data provides a unique opportunity to recast the pictorial level descriptions of biological processes in the language of mathematics, with the hope that such an undertaking will lead to deeper insights into the behavior of living systems. To achieve this end, we have undertaken three case studies in physical biology. In the first case study, we used statistical mechanics and polymer physics to construct a simple model that describes how flexible chains of amino acids, referred to as tethers, influence the information processing properties of signaling proteins. In the second case study, we studied the DNA ejection process of phage lambda in vitro. In particular, we used bulk and single-molecule methods to study the control parameters that govern the force and kinematics of the ejection process in vitro. In the last case study, we studied the DNA ejection process of phage lambda in vivo. We developed an assay that allows real-time monitoring of DNA ejection in vivo at the single-molecule level. We also developed a parallel system that allows the simultaneous visualization of both phage capsids and phage DNA at the single-cell level, constituting a true single-molecule Hershey-Chase experiment. The work described in this thesis outlines new tools, both in theory and experiment, that can be used to study biological systems as well as a paradigm that can be employed to mathematicize the cartoons of biology.

  14. Two-dimensional standing wave total internal reflection fluorescence microscopy: superresolution imaging of single molecular and biological specimens.

    Science.gov (United States)

    Chung, Euiheon; Kim, Daekeun; Cui, Yan; Kim, Yang-Hyo; So, Peter T C

    2007-09-01

    The development of high resolution, high speed imaging techniques allows the study of dynamical processes in biological systems. Lateral resolution improvement of up to a factor of 2 has been achieved using structured illumination. In a total internal reflection fluorescence microscope, an evanescence excitation field is formed as light is total internally reflected at an interface between a high and a low index medium. The excitation region resulting in low background fluorescence. We present even higher resolution wide-field biological imaging by use of standing wave total internal reflection fluorescence (SW-TIRF). Evanescent standing wave (SW) illumination is used to generate a sinusoidal high spatial frequency fringe pattern on specimen for lateral resolution enhancement. To prevent thermal drift of the SW, novel detection and estimation of the SW phase with real-time feedback control is devised for the stabilization and control of the fringe phase. SW-TIRF is a wide-field superresolution technique with resolution better than a fifth of emission wavelength or approximately 100 nm lateral resolution. We demonstrate the performance of the SW-TIRF microscopy using one- and two-directional SW illumination with a biological sample of cellular actin cytoskeleton of mouse fibroblast cells as well as single semiconductor nanocrystal molecules. The results confirm the superior resolution of SW-TIRF in addition to the merit of a high signal/background ratio from TIRF microscopy.

  15. [Radionuclide imaging in oral implantations. Personal experience in maxillary sinus elevation].

    Science.gov (United States)

    Dimonte, M; Inchingolo, F; Minonne, A; Stefanelli, M

    2000-11-01

    Presently nuclear medicine techniques are not very popular in oral implantology, but they can play an interesting role in this surgical field too. In particular bone scan with 99mTc-MDP allows to evaluate the function of oral implants and the survival of bone grafts. We report our experience with skull bone scan in maxillary sinus lifting. We performed a three-year follow-up on 13 patients treated with inlay-one stage uni- or bilateral sinus lifting with a mixture composed of 90% bovine bone powder and of 10% small bone splinters and autogenous fibrin glue. We performed imaging studies and quantitated implant MDP uptake from the mean values at the surgical site to the 5th neck vertebral ratio (M/V index). The M/V index was also statistically compared with the one measured in 13 patients with severe resorption of distal upper dental arches (bone height less than 0.5 cm) and in 63 patients with normal dental status. Scintigraphic data were interpreted in the light of clinical, radiological and histologic findings. All oral implants appeared to be fixed and radiographs showed good positioning and bone adhesion; bone height exceeded 1 cm. Peri implant biopsy material was formed by normal mature bone tissue without bovine bone granules, necrotic areas and inflammatory cells. The highest bone activity (M/V index: 1.54-2.57) was observed 1-4 months after sinus lifting. Then MDP uptake decreases and 18 months after surgery radionuclide uptake in maxillary arches is homogeneous, with M/V values of 0.81-0.88. The average M/V value in the 18 surgical sites was clearly higher than in the resorbed (1.44 vs 0.64; Kruskall-Wallis ANOVA test; Dunn's method; p < 0.05) and normal (1.44 vs 0.73; p < 0.05) maxillary arches. 99mTc-MDP can show the transformation of newformed into mature bone and then allows in vivo visualization of implant osteointegration. The importance of our work lies in the use of radionuclide imaging to assess both the function of oral implants inserted by a

  16. ATR-FTIR spectroscopic imaging: recent advances and applications to biological systems.

    Science.gov (United States)

    Kazarian, Sergei G; Chan, K L Andrew

    2013-04-07

    Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic imaging is a highly versatile, label free and non-destructive chemical imaging method which can be applied to study a wide range of samples and systems. This review summarises some of the recent advances and applications of this imaging method in the area of biomedical studies, including examples of section of aorta, skin tissue and live cells. Two of the major advantages of measuring in ATR mode are the opportunity to measure samples that absorb strongly in the IR spectrum, such as aqueous systems, without significant sample preparation and the ability to increase the spatial resolution of the measured image. The implications of these advantages as well as some limitations of this imaging approach are discussed and a brief outlook at some of the possible future developments in this area is provided.

  17. Color imaging of Mars by the High Resolution Imaging Science Experiment (HiRISE)

    Science.gov (United States)

    Delamere, W.A.; Tornabene, L.L.; McEwen, A.S.; Becker, K.; Bergstrom, J.W.; Bridges, N.T.; Eliason, E.M.; Gallagher, D.; Herkenhoff, K. E.; Keszthelyi, L.; Mattson, S.; McArthur, G.K.; Mellon, M.T.; Milazzo, M.; Russell, P.S.; Thomas, N.

    2010-01-01

    HiRISE has been producing a large number of scientifically useful color products of Mars and other planetary objects. The three broad spectral bands, coupled with the highly sensitive 14 bit detectors and time delay integration, enable detection of subtle color differences. The very high spatial resolution of HiRISE can augment the mineralogic interpretations based on multispectral (THEMIS) and hyperspectral datasets (TES, OMEGA and CRISM) and thereby enable detailed geologic and stratigraphic interpretations at meter scales. In addition to providing some examples of color images and their interpretation, we describe the processing techniques used to produce them and note some of the minor artifacts in the output. We also provide an example of how HiRISE color products can be effectively used to expand mineral and lithologic mapping provided by CRISM data products that are backed by other spectral datasets. The utility of high quality color data for understanding geologic processes on Mars has been one of the major successes of HiRISE. ?? 2009 Elsevier Inc.

  18. Justifying molecular images in cell biology textbooks: From constructions to primary data.

    Science.gov (United States)

    Serpente, Norberto

    2016-02-01

    For scientific claims to be reliable and productive they have to be justified. However, on the one hand little is known on what justification precisely means to scientists, and on the other the position held by philosophers of science on what it entails is rather limited; for justifications customarily refer to the written form (textual expressions) of scientific claims, leaving aside images, which, as many cases from the history of science show are relevant to this process. The fact that images can visually express scientific claims independently from text, plus their vast variety and origins, requires an assessment of the way they are currently justified and in turn used as sources to justify scientific claims in the case of particular scientific fields. Similarly, in view of the different nature of images, analysis is required to determine on what side of the philosophical distinction between data and phenomena these different kinds of images fall. This paper historicizes and documents a particular aspect of contemporary life sciences research: the use of the molecular image as vehicle of knowledge production in cell studies, a field that has undergone a significant shift in visual expressions from the early 1980s onwards. Focussing on textbooks as sources that have been overlooked in the historiography of contemporary biomedicine, the aim is to explore (1) whether the shift of cell studies, entailing a superseding of the optical image traditionally conceptualised as primary data, by the molecular image, corresponds with a shift of justificatory practices, and (2) to assess the role of the molecular image as primary data. This paper also explores the dual role of images as teaching resources and as resources for the construction of knowledge in cell studies especially in its relation to discovery and justification. Finally, this paper seeks to stimulate reflection on what kind of archival resources could benefit the work of present and future epistemic

  19. The Role of Consumer Experiences in Building the image of brands: A Study in Airlines

    Directory of Open Access Journals (Sweden)

    Ana Iris Tomás Vasconcelos

    2015-04-01

    Full Text Available Studies on brand and consumer experience gained emphasis from the twentieth century, however the relationship between these themes still has gaps. Therefore, this study examines the role of consumer experiences in building the brand image through the identification of thoughts, feelings and actions arising from consumer experiences with airlines, and the types of associations that the consumer makes such marks. Therefore, a variation of qualitative critical incident technique was used, considering those remembered experiences that have excelled in consumer perception, interviewing ten users of air services, based on a two parts semi-structured form: description of experiences with airlines and information about the image of the brands of airlines. The analyzed data have revealed that thoughts, feelings and actions arising from consumer experiences become important elements in shaping the perception of brands of airlines. Through the consumption experience, consumers mainly use the service attributes to build their perception of the marks of the airlines. These attributes are used either directly as to support other types of associations such as those related to company size.

  20. Biological implications of possible unattainability of comprehensive, molecular-resolution, real-time, volume imaging of the living cell

    CERN Document Server

    Okamoto, Hiroshi

    2016-01-01

    Despite the impressive advances in biological imaging, no imaging modality today generates, in a comprehensive manner, high-resolution images of crowded molecules working deep inside the living cell in real time. In this paper, instead of tackling this engineering problem in the hope of solving it, we ask a converse question: What if such imaging is \\emph{fundamentally} impossible? We argue that certain decoherence processes could be suppressed because the internal workings of the cell are not being closely "observed" in the quantum mechanical sense, as implied by the assumed impossibility of imaging. It is certainly true that the "wet and warm" living cell should not exhibit quantum behavior merely because of the lack of observation. Despite this, we plow ahead to see what \\emph{might} result from such absence of the outward flow of information. We suggest that chaotic dynamics in the cell could be quantum mechanically suppressed --- a known phenomenon in quantum chaology, which is potentially resistant to v...

  1. Clinical Experience With A High Resolution Digital Imaging System For Gastro-Intestinal Radiology

    Science.gov (United States)

    Edmonds, E. W.; Rowlands, J. A.; Hynes, D. M.; Toth, B. D.; Porter, A. J.

    1987-01-01

    In our department, it is planned that the gastro-intestinal fluoroscopic area will be equipped entirely with digital imaging systems. The use of the 1024 X 1024 pixel frame store, backed by a hard disc for rapid image transfer, and the production of hard copy on a laser imager has reached the point where clinical efficacy and acceptance are assured. The further addition of facilities for annotation and the application of digital post-processing techniques are being explored both at the clinical site and at the research laboratorieS. The use of laser imaging has produced a further improvement in image quality and some of the practical problems related to this apparatus will be described. The availability of larger capacity laser disc image storage enables the local area network or "mini-PACS" system for fluoroscopy areas to become a concept worthy of investigation. We present our experience over a number of years with these systems, together with our latest investigations into potential applications of laser technology to the practice of radiology in a busy imaging centre.

  2. Boundary Element Method for Reconstructing Absorption and Diffusion Coefficients of Biological Tissues in DOT/MicroCT Imaging.

    Science.gov (United States)

    Xie, Wenhao; Deng, Yong; Lian, Lichao; Yan, Dongmei; Yang, Xiaoquan; Luo, Qingming

    2016-01-01

    The functional information, the absorption and diffusion coefficients, as well as the structural information of biological tissues can be provided by the DOT(Diffuse Optical Tomograph)/MicroCT. In this paper, we use boundary element method to calculate the forward problem of DOT based on the structure prior given by the MicroCT, and then we reconstruct the absorption and diffusion coefficients of different biological tissues by the Levenberg-Marquardt algorithm. The method only needs surface meshing, reducing the complexity of calculation; in addition, it reconstructs a single value within an organ, which reduces the ill-posedness of the inverse problem to make reconstruction results have good noise stability. This indicates that the boundary element method-based reconstruction can serve as an new scheme for getting absorption and diffusion coefficients in DOT/MicroCT multimodality imaging.

  3. Changes in optical properties of biological tissue: experiment and Monte Carlo simulation

    Science.gov (United States)

    Kaspar, Pavel; Prokopyeva, Elena; Tománek, Pavel; Grmela, Lubomír.

    2016-12-01

    Biological tissue is a very complex, yet important material to describe and analyze. Its properties are affected by chemical processes too numerous to easily understand and describe. By simplifying and grouping some aspects together we are able to create a model for simulating behavior of a photon inside of a biological sample. Using the Monte Carlo method an algorithm for calculating photon propagation through the tissue based on several optical parameters, like absorption and scattering coefficients, refractive indices and optical anisotropy, can be created. Based on some of the results of the simulation a comparative measurement on a muscle sample was performed to prove the usefulness of such model and to describe changes in the tissue sample based on the aforementioned optical parameters in both real life and the simulation.

  4. Investigation of biological microstructures by using diffraction-enhanced imaging computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Shu Hang [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Graudate School of the Chinese Academy of Sciences, 100864 Beijing (China); Liu Bo [Capital University of Medical Sciences (China); Zhu, Peiping [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China)]. E-mail: zhupp@ihep.ac.cn; Gao Xin [Capital University of Medical Sciences (China); Yin Hongxia [Capital University of Medical Sciences (China); Yuan Qingxi [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Wang Junyue [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Graudate School of the Chinese Academy of Sciences, 100864 Beijing (China); Huang Wanxia [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China); Gao Xiulai [Capital University of Medical Sciences (China); Luo Shuqian [Capital University of Medical Sciences (China); Wu Ziyu [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China) and National Center for NanoScience and Technology (China)]. E-mail: wuzy@mail.ihep.ac.cn; Fang Shouxian [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, CAS, Beijing (China)

    2006-11-15

    Diffraction-enhanced imaging computer tomography (DEI-CT) is a new method to provide the object's inner information. Previous reports demonstrated its applicability in soft and hard tissue imaging. Here, we provide further evidence for the improved overall image quality and for the option to distinguish the inner microstructures of the guinea pig's cochlea. Data has shown the details of the cochlea's inner microstructure such as vestibular membrane which only have 6 {mu}m. A better knowledge of these microstructures may be relevant to achieve progress in the otology of clinical anatomization.

  5. Detecting myocardial ischemia with 2-D CVIB imaging method--an in vivo animal experiment study

    Institute of Scientific and Technical Information of China (English)

    JIANG Yong; BAI Jing; YING Kui; CHENG Kezheng; YU Can

    2004-01-01

    A 2-D cyclic variation of integrated backscatter (CVIB) imaging method was established for detecting myocardial ischemia. To demonstrate the feasibility and validity of this method, animal experiments were conducted. Acute myocardial ischemia was induced by occluding left anterior descending coronary artery in 10 anesthetized open-chest dogs. While scanning the normal hearts and the ischemic hearts with a B scanner, digital radiofrequency data were acquired by a real-time acquisition system in synchronism. The offline analysis to the radio-frequency signal with the 2-D CVIB imaging method was performed to verify the consistency between the imaging result and the design of the experiment. In addition, 4 dogs in experiment were treated with the heart pacemaker in order to investigate the influence of changing in heart rate on the detection of ischemic myocardium with the proposed method. The experimental result showed that the 2-D CVIB imaging method succeeded in detecting the ischemic myocardium and is a new non-invasive way for the cardiologists to both quantitatively and visually evaluate the contractile performance of the myocardium.

  6. Coherence Imaging Measurements of Impurity Flow in the Compact Toroidal Hybrid Experiment

    Science.gov (United States)

    Ennis, D. A.; Hartwell, G. J.; Johnson, C. A.; Maurer, D. A.; Allen, S. L.; Meyer, W. H.; Samuell, C. M.

    2016-10-01

    Measurements of impurity ion emissivity and velocity in the Compact Toroidal Hybrid (CTH) experiment are achieved with a new optical coherence imaging diagnostic. The Coherence Imaging Spectroscopy (CIS) technique measures the spectral coherence of an emission line with an imaging interferometer of fixed delay. CIS has a number of advantages when compared to dispersive Doppler spectroscopy, including higher throughput and the capability to provide 2D spectral images, making it ideal for investigating the non-axisymmetric geometry of CTH plasmas. Furthermore, detailed measurements of the ion flow structure provided by CIS combined with predictive computational models could also provide spatially resolved images of complex flow structures, such as those associated with an island divertor. First CIS measurements of CTH plasmas reveal strong signals for C III (465 nm), He II (468 nm) and C II (513 nm) emission. Preliminary analysis of C III interferograms indicate a net toroidal flow on the order of 10 km/s during the time of peak current. Bench tests using Zn and Cd light sources reveal that the temperature of the instrument must be actively controlled to within 0.01°C to limit phase drift of the interferometer resulting in artificially measured flow. Results from this diagnostic will aid in characterizing the ion flow in planned island divertor and MHD mode-locking experiments. Work supported by USDoE Grant DE-FG02-00ER54610.

  7. The protoMIRAX Hard X-ray Imaging Balloon Experiment

    CERN Document Server

    Braga, João; Avila, Manuel A C; Penacchioni, Ana V; Sacahui, J Rodrigo; Santiago, Valdivino A de; Mattiello-Francisco, Fátima; Strauss, Cesar; Fialho, Márcio A A

    2015-01-01

    The protoMIRAX hard X-ray imaging telescope is a balloon-borne experiment developed as a pathfinder for the MIRAX satellite mission. The experiment consists essentially in a coded-aperture hard X-ray (30-200 keV) imager with a square array (13$\\times$13) of 2mm-thick planar CZT detectors with a total area of 169 cm$^2$. The total, fully-coded field-of-view is $21^{\\circ}\\times 21^{\\circ}$ and the angular resolution is 1$^{\\circ}$43'. In this paper we describe the protoMIRAX instrument and all the subsystems of its balloon gondola, and we show simulated results of the instrument performance. The main objective of protoMIRAX is to carry out imaging spectroscopy of selected bright sources to demonstrate the performance of a prototype of the MIRAX hard X-ray imager. Detailed background and imaging simulations have been performed for protoMIRAX balloon flights. The 3$\\sigma$ sensitivity for the 30-200 keV range is ~1.9 $\\times$ 10$^{-5}$ photons cm$^{-2}$ s$^{-1}$ for an integration time of 8 hs at an atmospheric ...

  8. Phase retrieval deblurring for imaging of dense object within a low scattering soft biological tissue

    Science.gov (United States)

    Shalev, Maya Aviv; Rivenson, Yair; Meiri, Amihai; Zalevsky, Zeev

    2016-09-01

    Tissues are characterized by a strong scattering of visible optical radiation, which prevents one from achieving deep-tissue imaging. We propose a computational imaging technique for the inference of specific macroscopic, spatial phase distribution features of the scattering media. The spatial phase distribution is reconstructed from several defocused intensity images. We empirically demonstrate the method by reconstructing the location of two fibula chicken bones, embedded within chicken breast tissue. The suggested technique is safe, using visible laser illumination, and noninvasive. It is also cost-effective since a simple optical system is used and the images are acquired using a conventional camera, and it does not require interferometric detection as well as direct access to the object in absence of the layer.

  9. Recent Advance of Biological Molecular Imaging Based on Lanthanide-Doped Upconversion-Luminescent Nanomaterials

    Directory of Open Access Journals (Sweden)

    Yuanzeng Min

    2014-02-01

    Full Text Available Lanthanide-doped upconversion-luminescent nanoparticles (UCNPs, which can be excited by near-infrared (NIR laser irradiation to emit multiplex light, have been proven to be very useful for in vitro and in vivo molecular imaging studies. In comparison with the conventionally used down-conversion fluorescence imaging strategies, the NIR light excited luminescence of UCNPs displays high photostability, low cytotoxicity, little background auto-fluorescence, which allows for deep tissue penetration, making them attractive as contrast agents for biomedical imaging applications. In this review, we will mainly focus on the latest development of a new type of lanthanide-doped UCNP material and its main applications for in vitro and in vivo molecular imaging and we will also discuss the challenges and future perspectives.

  10. Molecular imaging of brain tumors personal experience and review of the literature.

    Science.gov (United States)

    Schaller, Bernhard J; Cornelius, Jan F; Sandu, Nora; Buchfelder, Michael

    2008-12-01

    HSV-1-TK expression if the blood brain barrier is disrupted. The higher uptake of [(18)F]FLT in the wild-type compared to the transduced type may demonstrate the different doubling time of both tumor tissues suggesting different cytosolic thymidine kinase activity. Molecular imaging probes are developed to image the function of targets without disturbing them or as drug in oder to modify the target's function. This is transfer of gene therapy's experimental knowledge into clinical applications. Molecular imaging closes the gap between in vitro to in vivo integrative biology of disease.

  11. Progress Toward a Thermal-Hydrological-Mechanical-Chemical-Biological (THMCB) Experiment in the Homestake Mine Deep Underground Science and Engineering Laboratory

    Science.gov (United States)

    Sonnenthal, E. L.; Maher, K.; Elsworth, D.; Lowell, R. P.; Uzunlar, N.; Mailloux, B. J.; Conrad, M. E.; Olsen, N. J.; Jones, T. L.; Cruz, M. F.; Torchinsky, A.

    2011-12-01

    The purpose of performing a long-term hydrothermal experiment in a deep mine is to gain a scientific understanding of the coupled physical, chemical, and biological processes taking place in fractured rock under the influence of mechanical stress, thermal effects, and fluid flow. Only in a controlled experiment in a well-characterized rock mass, can a fractured rock be probed in 3-D through geophysical imaging, in situ measurements, geochemical/biological sampling, and numerical modeling. Our project is focused on the feasibility of a THMCB experiment in the Homestake Mine, South Dakota to study the long-term evolution (10+ years) of a perturbed heterogeneous rock mass. In addition to the experiment as a laboratory for studying crustal processes, it has direct application to Enhanced Geothermal Systems, carbon sequestration, and contaminant transport. Field activities have focused on fracture and feature mapping, flux measurements from flowing fractures, and collection of water and rock samples for geochemical, biological, and isotopic analyses. Fracture mapping and seepage measurements are being used to develop estimates of permeability and fluxes at different length scales and design the location and orientation of the heater array. Fluxes measured up to several liters/minute indicate localized regions of very high fracture permeability, likely in excess of 10-10 m2. Isotopic measurements indicate heterogeneity in the fracture network on the scale of tens of meters in addition to the large-scale geochemical heterogeneity observed in the mine. New methods for sampling and filtering water samples were developed and tested with the goal of performing radiocarbon analyses in DNA and phospholipid fatty acids. Analytical and numerical models of the thermal perturbation have been used to design the heater orientation and spacing. Reaction path and THC simulations were performed to assess geochemical and porosity/permeability changes as a function of the heat input

  12. Method for Separation of Blood Vessels on the Three-Color Images of Biological Tissues

    Science.gov (United States)

    Lisenko, S. A.

    2017-07-01

    A new technology was developed to improve the visibility of blood vessels on images of tissues of hollow human organs(the alimentary tract and respiratory system) based on the relation between the color components of the image, the scattering properties of the tissue, and its hemoglobin content. A statistical operator was presented to convert the three-color image of the tissue into a parametric map objectively characterizing the concentration of hemoglobin in the tissue regardless of the illumination and shooting conditions. An algorithm for obtaining conversion parameters for image systems with known spectral characteristics was presented. An image of a multilayer multiple-scattering medium modeling bronchial tissue was synthesized and was used to evaluate the efficiency of the proposed conversion system. It was shown that the conversion made it possible to increase the contrast of the blood vessels by almost two orders of magnitude, to significantly improve the clarity of the display of their borders, and to eliminate almost completely the influence of background and nonuniform illumination of the medium in comparison with the original image.

  13. Imaging cleared intact biological systems at a cellular level by 3DISCO.

    Science.gov (United States)

    Ertürk, Ali; Lafkas, Daniel; Chalouni, Cecile

    2014-07-07

    Tissue clearing and subsequent imaging of transparent organs is a powerful method to analyze fluorescently labeled cells and molecules in 3D, in intact organs. Unlike traditional histological methods, where the tissue of interest is sectioned for fluorescent imaging, 3D imaging of cleared tissue allows examination of labeled cells and molecules in the entire specimen. To this end, optically opaque tissues should be rendered transparent by matching the refractory indices throughout the tissue. Subsequently, the tissue can be imaged at once using laser-scanning microscopes to obtain a complete high-resolution 3D image of the specimen. A growing list of tissue clearing protocols including 3DISCO, CLARITY, Sca/e, ClearT2, and SeeDB provide new ways for researchers to image their tissue of interest as a whole. Among them, 3DISCO is a highly reproducible and straightforward method, which can clear different types of tissues and can be utilized with various microscopy techniques. This protocol describes this straightforward procedure and presents its various applications. It also discusses the limitations and possible difficulties and how to overcome them.

  14. Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.

    Directory of Open Access Journals (Sweden)

    David A Van Valen

    2016-11-01

    Full Text Available Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domains of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.

  15. A New Sample Substrate for Imaging and Correlating Organic and Trace Metal Composition in Biological Cells and Tissues

    Energy Technology Data Exchange (ETDEWEB)

    Miller,L.; Wang, Q.; Smith, R.; Zhong, H.; Elliott, D.; Warren, J.

    2007-01-01

    Many disease processes involve alterations in the chemical makeup of tissue. Synchrotron-based infrared (IR) and X-ray fluorescence (XRF) microscopes are becoming increasingly popular tools for imaging the organic and trace metal compositions of biological materials, respectively, without the need for extrinsic labels or stains. Fourier transform infrared microspectroscopy (FTIRM) provides chemical information on the organic components of a material at a diffraction-limited spatial resolution of 2-10 {mu}m in the mid-infrared region. The synchrotron X-ray fluorescence (SXRF) microprobe is a complementary technique used to probe trace element content in the same systems with a similar spatial resolution. However to be most beneficial, it is important to combine the results from both imaging techniques on a single sample, which requires precise overlap of the IR and X-ray images. In this work, we have developed a sample substrate containing a gold grid pattern on its surface, which can be imaged with both the IR and X-ray microscopes. The substrate consists of a low trace element glass slide that has a gold grid patterned on its surface, where the major and minor parts of the grid contain 25 and 12 nm gold, respectively. This grid pattern can be imaged with the IR microscope because the reflectivity of gold differs as a function of thickness. The pattern can also be imaged with the SXRF microprobe because the Au fluorescence intensity changes with gold thickness. The tissue sample is placed on top of the patterned substrate. The grid pattern's IR reflectivity image and the gold SXRF image are used as fiducial markers for spatially overlapping the IR and SXRF images from the tissue. Results show that IR and X-ray images can be correlated precisely, with a spatial resolution of less than one pixel (i.e., 2-3 microns). The development of this new tool will be presented along with applications to paraffin-embedded metalloprotein crystals, Alzheimer's disease

  16. A radio-frequency system for in vivo pilot experiments aimed at the studies on biological effects of electromagnetic fields.

    Science.gov (United States)

    Ardoino, Lucia; Lopresto, Vanni; Mancini, Sergio; Marino, Carmela; Pinto, Rosanna; Lovisolo, Giorgio A

    2005-08-07

    An exposure system consisting of two long transversal electromagnetic (TEM) cells, operating at a frequency of 900 MHz, is presented and discussed. The set-up allows simultaneous exposure of a significant number of animals (up to 12 mice per cell) in a blind way to a uniform plane wave at a frequency of 900 MHz, for investigating possible biological effects of exposure to electromagnetic fields produced by wireless communication systems. A heating/refrigerating system has also been designed for maintaining comfortable environmental conditions within the TEM cells during experiments. An accurate dosimetric study has been performed both numerically and by means of direct measurements on phantoms and living mice. The results have shown that good homogeneity of exposure and adequate power efficiency, in terms of whole-body specific absorption rate (SAR) per 1 W of input power, are achievable for the biological target.

  17. Fabrication of aggregation-induced emission based fluorescent nanoparticles and their biological imaging application: recent progress and perspectives

    Directory of Open Access Journals (Sweden)

    Bin Yang

    2016-06-01

    Full Text Available Aggregation-induced emission (AIE dyes have received wide-spread concern since their inception. Several types of AIE-based fluorescent nanoparticle (FNP have been developed, and the potential applications of these FNPs have also been explored. Recent studies of AIE-based FNPs in biological areas have suggested that they show promise as bio-materials for cell imaging and other biomedical applications. This article reviews recent progress in the synthesis of AIE-based FNPs via non-covalent, covalent and novel one-pot strategies, and the subsequent cell-imaging of those AIE-based FNPs. Many successes have been achieved, and there is still plenty of space for the development of AIE-based FNPs as new bio-materials.

  18. Towards tender X-rays with Zernike phase-contrast imaging of biological samples at 50 nm resolution.

    Science.gov (United States)

    Vartiainen, Ismo; Warmer, Martin; Goeries, Dennis; Herker, Eva; Reimer, Rudolph; David, Christian; Meents, Alke

    2014-07-01

    X-ray microscopy is a commonly used method especially in material science application, where the large penetration depth of X-rays is necessary for three-dimensional structural studies of thick specimens with high-Z elements. In this paper it is shown that full-field X-ray microscopy at 6.2 keV can be utilized for imaging of biological specimens with high resolution. A full-field Zernike phase-contrast microscope based on diffractive optics is used to study lipid droplet formation in hepatoma cells. It is shown that the contrast of the images is comparable with that of electron microscopy, and even better contrast at tender X-ray energies between 2.5 keV and 4 keV is expected.

  19. Vehicle occupancy detection camera position optimization using design of experiments and standard image references

    Science.gov (United States)

    Paul, Peter; Hoover, Martin; Rabbani, Mojgan

    2013-03-01

    Camera positioning and orientation is important to applications in domains such as transportation since the objects to be imaged vary greatly in shape and size. In a typical transportation application that requires capturing still images, inductive loops buried in the ground or laser trigger sensors are used when a vehicle reaches the image capture zone to trigger the image capture system. The camera in such a system is in a fixed position pointed at the roadway and at a fixed orientation. Thus the problem is to determine the optimal location and orientation of the camera when capturing images from a wide variety of vehicles. Methods from Design for Six Sigma, including identifying important parameters and noise sources and performing systematically designed experiments (DOE) can be used to determine an effective set of parameter settings for the camera position and orientation under these conditions. In the transportation application of high occupancy vehicle lane enforcement, the number of passengers in the vehicle is to be counted. Past work has described front seat vehicle occupant counting using a camera mounted on an overhead gantry looking through the front windshield in order to capture images of vehicle occupants. However, viewing rear seat passengers is more problematic due to obstructions including the vehicle body frame structures and seats. One approach is to view the rear seats through the side window. In this situation the problem of optimally positioning and orienting the camera to adequately capture the rear seats through the side window can be addressed through a designed experiment. In any automated traffic enforcement system it is necessary for humans to be able to review any automatically captured digital imagery in order to verify detected infractions. Thus for defining an output to be optimized for the designed experiment, a human defined standard image reference (SIR) was used to quantify the quality of the line-of-sight to the rear seats of

  20. Microscopy Images as Interactive Tools in Cell Modeling and Cell Biology Education

    Science.gov (United States)

    Araujo-Jorge, Tania C.; Cardona, Tania S.; Mendes, Claudia L. S.; Henriques-Pons, Andrea; Meirelles, Rosane M. S.; Coutinho, Claudia M. L. M.; Aguiar, Luiz Edmundo V.; Meirelles, Maria de Nazareth L.; de Castro, Solange L.; Barbosa, Helene S.; Luz, Mauricio R. M. P.

    2004-01-01

    The advent of genomics, proteomics, and microarray technology has brought much excitement to science, both in teaching and in learning. The public is eager to know about the processes of life. In the present context of the explosive growth of scientific information, a major challenge of modern cell biology is to popularize basic concepts of…

  1. The image simulation arithmetic of the degradating process of porous biologic ceramic in life-form

    Institute of Scientific and Technical Information of China (English)

    CHEN Zuo-bing; HUANG Jian-zhong; YAN Yu-hua; LI Shi-pu

    2001-01-01

    @@ It is a complex and difficult task to simulate the degradating process of porous biologic ceramic in life-form by computer. Because the evolvement of crystal' s structure deals with not only the mechanism of many factors, such as crystallography tropism, the reciprocity of wafer, interfacial movement, but also topology geometry mechanism of dimensional padding.

  2. Hemispherical Brillouin zone imaging of a diamond-type biological photonic crystal

    NARCIS (Netherlands)

    Wilts, Bodo D.; Michielsen, Kristel; De Raedt, Hans; Stavenga, Doekele G.

    2012-01-01

    The brilliant structural body colours of many animals are created by three-dimensional biological photonic crystals that act as wavelength-specific reflectors. Here, we report a study on the vividly coloured scales of the diamond weevil, Entimus imperialis. Electron microscopy identified the chitin

  3. Hemispherical Brillouin zone imaging of a diamond-type biological photonic crystal

    NARCIS (Netherlands)

    Wilts, Bodo D.; Michielsen, Kristel; De Raedt, Hans; Stavenga, Doekele G.

    2012-01-01

    The brilliant structural body colours of many animals are created by three-dimensional biological photonic crystals that act as wavelength-specific reflectors. Here, we report a study on the vividly coloured scales of the diamond weevil, Entimus imperialis. Electron microscopy identified the chitin

  4. Development and Application of Raman Microspectroscopic and Raman Imaging Techniques for Cell Biological Studies

    NARCIS (Netherlands)

    PUPPELS, G J; SCHUT, T C B; SIJTSEMA, N M; GROND, M; MARABOEUF, F; DEGRAUW, C G; FIGDOR, C G; GREVE, J

    1995-01-01

    Raman spectroscopy is being used to study biological molecules for some three decades now. Thanks to continuing advances in instrumentation more and more applications have become feasible in which molecules are studied in situ, and this has enabled Raman spectroscopy to enter the realms of

  5. The Lyman Alpha Imaging-Monitor Experiment (LAIME) for TESIS/CORONAS-PHOTON

    Science.gov (United States)

    Damé, L.; Koutchmy, S.; Kuzin, S.; Lamy, P.; Malherbe, J.-M.; Noëns, J.-C.

    LAIME the Lyman Alpha Imaging-Monitor Experiment is a remarkably simple no mechanisms and compact 100x100x400 mm full Sun imager to be flown with TESIS on the CORONAS-PHOTON mission launch expected before mid-2008 As such it will be the only true chromospheric imager to be flown in the next years supporting TESIS EUV-XUV imaging SDO and the Belgian LYRA Lyman Alpha flux monitor on the ESA PROBA-2 microsatellite launch expected in September 2007 We will give a short description of this unique O60 mm aperture imaging telescope dedicated to the investigating of the magnetic sources of solar variability in the UV and chromospheric and coronal disruptive events rapid waves Moreton waves disparitions brusques of prominences filaments eruptions and CMEs onset The resolution pixel is 2 7 arcsec the field of view 1 4 solar radius and the acquisition cadence could be as high as 1 image minute The back thinned E2V CCD in the focal plane is using frame transfer to avoid shutter and mechanisms Further more the double Lyman Alpha filtering allows a 40 AA FWHM bandwidth and excellent rejection yet providing a vacuum seal design of the telescope MgF2 entrance window Structural stability of the telescope focal length 1 m is preserved by a 4-INVAR bars design with Aluminium compensation in a large pm 10 o around 20 o

  6. Clean localization super-resolution microscopy for 3D biological imaging

    Energy Technology Data Exchange (ETDEWEB)

    Mondal, Partha P., E-mail: partha@iap.iisc.ernet.in [Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012 (India); Curthoys, Nikki M.; Hess, Samuel T. [Department of Physics and Astronomy, University of Maine, Orono, Maine 04469 (United States)

    2016-01-15

    We propose clean localization microscopy (a variant of fPALM) using a molecule filtering technique. Localization imaging involves acquiring a large number of images containing single molecule signatures followed by one-to-one mapping to render a super-resolution image. In principle, this process can be repeated for other z-planes to construct a 3D image. But, single molecules observed from off-focal planes result in false representation of their presence in the focal plane, resulting in incorrect quantification and analysis. We overcome this with a single molecule filtering technique that imposes constraints on the diffraction limited spot size of single molecules in the image plane. Calibration with sub-diffraction size beads puts a natural cutoff on the actual diffraction-limited size of single molecules in the focal plane. This helps in distinguishing beads present in the focal plane from those in the off-focal planes thereby providing an estimate of the single molecules in the focal plane. We study the distribution of actin (labeled with a photoactivatable CAGE 552 dye) in NIH 3T3 mouse fibroblast cells.

  7. Label-Free Acetylcholine Image Sensor Based on Charge Transfer Technology for Biological Phenomenon Tracking

    Science.gov (United States)

    Takenaga, Shoko; Tamai, Yui; Okumura, Koichi; Ishida, Makoto; Sawada, Kazuaki

    2012-02-01

    A 32 ×32 charge-transfer enzyme-type acetylcholine (ACh) image sensor array was produced for label-free tracking of images of ACh distribution and its performance in repeatable measurements without enzyme deactivation was examined. The proposed sensor was based on a charge-transfer-type pH image sensor, which was modified using an enzyme membrane (acetylcholine esterase, AChE) for each pixel. The ACh image sensor detected hydrogen ions generated by the ACh-AChE reaction. A polyion complex membrane composed of poly(L-lysine) and poly(4-styrenesulfonate) was used to immobilize the enzyme on the sensor. The improved uniformity and adhesion of the polyion complex membrane were evaluated in this study. As a result, temporal and spatial fluctuations of the ACh image sensor were successfully minimized using this approach. The sensitivity of the sensor was 4.2 mV/mM, and its detection limit was 20 µM. In five repeated measurements, the repeatability was 8.8%.

  8. Quantitative analysis of biological tissues using Fourier transform-second-harmonic generation imaging

    Science.gov (United States)

    Ambekar Ramachandra Rao, Raghu; Mehta, Monal R.; Toussaint, Kimani C., Jr.

    2010-02-01

    We demonstrate the use of Fourier transform-second-harmonic generation (FT-SHG) imaging of collagen fibers as a means of performing quantitative analysis of obtained images of selected spatial regions in porcine trachea, ear, and cornea. Two quantitative markers, preferred orientation and maximum spatial frequency are proposed for differentiating structural information between various spatial regions of interest in the specimens. The ear shows consistent maximum spatial frequency and orientation as also observed in its real-space image. However, there are observable changes in the orientation and minimum feature size of fibers in the trachea indicating a more random organization. Finally, the analysis is applied to a 3D image stack of the cornea. It is shown that the standard deviation of the orientation is sensitive to the randomness in fiber orientation. Regions with variations in the maximum spatial frequency, but with relatively constant orientation, suggest that maximum spatial frequency is useful as an independent quantitative marker. We emphasize that FT-SHG is a simple, yet powerful, tool for extracting information from images that is not obvious in real space. This technique can be used as a quantitative biomarker to assess the structure of collagen fibers that may change due to damage from disease or physical injury.

  9. Biological therapies for the treatment of juvenile idiopathic arthritis: Lessons from the adult and pediatric experiences

    Directory of Open Access Journals (Sweden)

    Matthew L Stoll

    2008-06-01

    Full Text Available Matthew L Stoll, Alisa C GotteDepartment of Pediatrics, Division of Rheumatology, UT Southwestern Medical Center, Dallas, TX, USAAbstract: Biologics have advanced the therapy of adult and pediatric arthritis. They have been linked to rare serious adverse outcomes, but the actual risk of these events is controversial in adults, and largely unknown in pediatrics. Because of the paucity of safety and efficacy data in children, pediatric rheumatologists often rely on the adult literature. Herein, we reviewed the adult and pediatric literature on five classes of medicines: Tumor necrosis factor (TNF inhibitors, anakinra, rituximab, abatacept, and tocilizumab. For efficacy, we reviewed randomized controlled studies in adults, but did include lesser qualities of evidence for pediatrics. For safety, we utilized prospective and retrospective studies, rarely including reports from other inflammatory conditions. The review included studies on rheumatoid arthritis and spondyloarthritis, as well as juvenile idiopathic arthritis. Overall, we found that the TNF inhibitors have generally been found safe and effective in adult and pediatric use, although risks of infections and other adverse events are discussed. Anakinra, rituximab, abatacept, and tocilizumab have also shown positive results in adult trials, but there is minimal pediatric data published with the exception of small studies involving the subgroup of children with systemic onset juvenile idiopathic arthritis, in whom anakinra and tocilizumab may be effective therapies.Keywords: juvenile idiopathic arthritis, biologics, rheumatoid arthritis

  10. A Case-Based Scenario with Interdisciplinary Guided-Inquiry in Chemistry and Biology: Experiences of First Year Forensic Science Students

    Science.gov (United States)

    Cresswell, Sarah L.; Loughlin, Wendy A.

    In this paper, insight into forensic science students' experiences of a case-based scenario with an interdisciplinary guided-inquiry experience in chemistry and biology is presented. Evaluation of student experiences and interest showed that the students were engaged with all aspects of the case-based scenario, including the curriculum theory…

  11. The Cosmic Infrared Background Experiment (CIBER): The Wide-Field Imagers

    CERN Document Server

    Bock, J; Arai, T; Battle, J; Cooray, A; Hristov, V; Keating, B; Kim, M G; Lam, A C; Lee, D H; Levenson, L R; Mason, P; Matsumoto, T; Matsuura, S; Mitchell-Wynne, K; Nam, U W; Renbarger, T; Smidt, J; Suzuki, K; Tsumura, K; Wada, T; Zemcov, M

    2012-01-01

    We have developed and characterized an imaging instrument to measure the spatial properties of the diffuse near-infrared extragalactic background light in a search for fluctuations from z > 6 galaxies during the epoch of reionization. The instrument is part of the Cosmic Infrared Background Experiment (CIBER), designed to observe the extragalactic background light above the Earth's atmosphere during a suborbital sounding rocket flight. The imaging instrument incorporates a 2x2 degree field of view, to measure fluctuations over the predicted peak of the spatial power spectrum at 10 arcminutes, and 7"x7" pixels, to remove lower redshift galaxies to a depth sufficient to reduce the low-redshift galaxy clustering foreground below instrumental sensitivity. The imaging instrument employs two cameras with \\Delta \\lambda / \\lambda ~0.5 bandpasses centered at 1.1 and 1.6 microns to spectrally discriminate reionization extragalactic background fluctuations from local foreground fluctuations. CIBER operates at wavelengt...

  12. First downscattered neutron images from Inertial Confinement Fusion experiments at the National Ignition Facility

    Directory of Open Access Journals (Sweden)

    Guler Nevzat

    2013-11-01

    Full Text Available Inertial Confinement Fusion experiments at the National Ignition Facility (NIF are designed to understand and test the basic principles of self-sustaining fusion reactions by laser driven compression of deuterium-tritium (DT filled cryogenic plastic (CH capsules. The experimental campaign is ongoing to tune the implosions and characterize the burning plasma conditions. Nuclear diagnostics play an important role in measuring the characteristics of these burning plasmas, providing feedback to improve the implosion dynamics. The Neutron Imaging (NI diagnostic provides information on the distribution of the central fusion reaction region and the surrounding DT fuel by collecting images at two different energy bands for primary (13–15 MeV and downscattered (10–12 MeV neutrons. From these distributions, the final shape and size of the compressed capsule can be estimated and the symmetry of the compression can be inferred. The first downscattered neutron images from imploding ICF capsules are shown in this paper.

  13. High-resolution X-ray imaging in fast ignition experiment using Gekko and LFEX lasers

    Directory of Open Access Journals (Sweden)

    Koga M.

    2013-11-01

    Full Text Available We improved diagnostic instruments to measure X-ray images in a hard X-ray harsh environment and succeeded in obtaining clear images with X-ray framing camera and X-ray streak camera in fast ignition experiment conducted in 2011 (FG-02 Experimental Campaign. We found that high-energy X-ray signals could be used as an indicator of the LFEX laser injection time relative to the imploded core. The LFEX laser injection time was estimated with better than 10 ps accuracy. Time-resolved 2D X-ray images suggested that shapes and motions of imploded core plasmas were improved by changing the configuration of the implosion lasers.

  14. Diffraction enhanced imaging and x-ray fluorescence microtomography for analyzing biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, H.S.; Pereira, G.R.; Lopes, R.T. [Laboratorio de Instrumentacao Nuclear-COPPE/UFRJ-RJ (Brazil); Anjos, M.J. [Instituto de Fisica-UERJ-RJ (Brazil); Faria, P. [Instituto Nacional do Cancer-INCa-RJ (Brazil); Kellermann, G.; Perez, C.A. [Laboratorio Nacional de Luz Sincrotron-Campinas-SP (Brazil); Tirao, G. [Faculdad de Mat. Astronomia y Fisica (FAMAF), UNC. Cordoba (Argentina); Mazzaro, I. [Laboratorio de Optica de Raios X e Instrumentacao-UFPR-Curitiba-PR (Brazil); Giles, C. [Laboratorio de Cristalografia Aplicada e Raios X-UNICAMP-Campinas-SP (Brazil)

    2007-07-15

    In this work, breast tissue samples were investigated in order to verify the distribution of certain elements by x-ray fluorescence computed tomography (XRFCT) correlated with the characteristics and pathology of each tissue observed by diffraction enhanced imaging (DEI). The DEI system can show details in low attenuation tissues. It is based on the contrast imaging obtained by extinction, diffraction and refraction characteristics and can improve reduction in false positive and false negative diagnoses. XRFCT allows mapping of all elements within the sample, since even a minute fluorescence signal can be detected. DEI imaging techniques revealed the complex structure of the disease, confirmed by the histological section, and showed microstructures in all planes of the sample. The XRFCT showed the distribution of Zn, Cu and Fe at higher concentration. (authors)

  15. Selective-plane illumination microscopy for high-content volumetric biological imaging

    Science.gov (United States)

    McGorty, Ryan; Huang, Bo

    2016-03-01

    Light-sheet microscopy, also named selective-plane illumination microscopy, enables optical sectioning with minimal light delivered to the sample. Therefore, it allows one to gather volumetric datasets of developing embryos and other light-sensitive samples over extended times. We have configured a light-sheet microscope that, unlike most previous designs, can image samples in formats compatible with high-content imaging. Our microscope can be used with multi-well plates or with microfluidic devices. In designing our optical system to accommodate these types of sample holders we encounter large optical aberrations. We counter these aberrations with both static optical components in the imaging path and with adaptive optics. Potential applications of this microscope include studying the development of a large number of embryos in parallel and over long times with subcellular resolution and doing high-throughput screens on organisms or cells where volumetric data is necessary.

  16. Vibrational spectroscopic imaging of living systems: An emerging platform for biology and medicine.

    Science.gov (United States)

    Cheng, Ji-Xin; Xie, X Sunney

    2015-11-27

    Vibrational spectroscopy has been extensively applied to the study of molecules in gas phase, in condensed phase, and at interfaces. The transition from spectroscopy to spectroscopic imaging of living systems, which allows the spectrum of biomolecules to act as natural contrast, is opening new opportunities to reveal cellular machinery and to enable molecule-based diagnosis. Such a transition, however, involves more than a simple combination of spectrometry and microscopy. We review recent efforts that have pushed the boundary of the vibrational spectroscopic imaging field in terms of spectral acquisition speed, detection sensitivity, spatial resolution, and imaging depth. We further highlight recent applications in functional analysis of single cells and in label-free detection of diseases. Copyright © 2015, American Association for the Advancement of Science.

  17. A combined method for correlative 3D imaging of biological samples from macro to nano scale

    Science.gov (United States)

    Kellner, Manuela; Heidrich, Marko; Lorbeer, Raoul-Amadeus; Antonopoulos, Georgios C.; Knudsen, Lars; Wrede, Christoph; Izykowski, Nicole; Grothausmann, Roman; Jonigk, Danny; Ochs, Matthias; Ripken, Tammo; Kühnel, Mark P.; Meyer, Heiko

    2016-10-01

    Correlative analysis requires examination of a specimen from macro to nano scale as well as applicability of analytical methods ranging from morphological to molecular. Accomplishing this with one and the same sample is laborious at best, due to deformation and biodegradation during measurements or intermediary preparation steps. Furthermore, data alignment using differing imaging techniques turns out to be a complex task, which considerably complicates the interconnection of results. We present correlative imaging of the accessory rat lung lobe by combining a modified Scanning Laser Optical Tomography (SLOT) setup with a specially developed sample preparation method (CRISTAL). CRISTAL is a resin-based embedding method that optically clears the specimen while allowing sectioning and preventing degradation. We applied and correlated SLOT with Multi Photon Microscopy, histological and immunofluorescence analysis as well as Transmission Electron Microscopy, all in the same sample. Thus, combining CRISTAL with SLOT enables the correlative utilization of a vast variety of imaging techniques.

  18. Women’s experiences and preferences regarding breast imaging after completing breast cancer treatment

    Directory of Open Access Journals (Sweden)

    Brandzel S

    2017-02-01

    Full Text Available Susan Brandzel,1 Dori E Rosenberg,1 Dianne Johnson,1 Mary Bush,1 Karla Kerlikowske,2–5 Tracy Onega,6,7 Louise Henderson,8 Larissa Nekhlyudov,9,10 Wendy DeMartini,11 Karen J Wernli1 1Group Health Research Institute, Group Health Cooperative, Seattle, WA, 2Department of Medicine, 3Department of Epidemiology, 4Department of Biostatistics, 5Department of Veterans Affairs, University of California, San Francisco, San Francisco, CA, 6Department of Biomedical Data Science, 7Department of Epidemiology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 8Department of Radiology, University of North Carolina, Chapel Hill, NC, 9Department of Population Medicine, Harvard Medical School, 10Department of Medicine, Brigham and Women’s Hospital, Boston, MA, 11Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA Background: After treatment for breast cancer, most women receive an annual surveillance mammography to look for subsequent breast cancers. Supplemental breast MRI is sometimes used in addition to mammography despite the lack of clinical evidence for it. Breast imaging after cancer treatment is an emotionally charged experience, an important part of survivorship care, and a topic about which limited patient information exists. We assessed women’s experiences and preferences about breast cancer surveillance imaging with the goal of determining where gaps in care and knowledge could be filled. Participants and methods: We conducted six focus groups with a convenience sample of 41 women in California, North Carolina, and New Hampshire (USA. Participants were aged 38–75 years, had experienced stage 0–III breast cancer within the previous 5 years, and had completed initial treatment. We used inductive thematic analysis to identify key themes from verbatim transcripts. Results: Women reported various types and frequencies of surveillance imaging and a range of surveillance imaging

  19. Solid Hydrogen Experiments for Atomic Propellants: Particle Formation, Imaging, Observations, and Analyses

    Science.gov (United States)

    Palaszewski, Bryan

    2005-01-01

    This report presents particle formation observations and detailed analyses of the images from experiments that were conducted on the formation of solid hydrogen particles in liquid helium. Hydrogen was frozen into particles in liquid helium, and observed with a video camera. The solid hydrogen particle sizes and the total mass of hydrogen particles were estimated. These newly analyzed data are from the test series held on February 28, 2001. Particle sizes from previous testing in 1999 and the testing in 2001 were similar. Though the 2001 testing created similar particles sizes, many new particle formation phenomena were observed: microparticles and delayed particle formation. These experiment image analyses are some of the first steps toward visually characterizing these particles, and they allow designers to understand what issues must be addressed in atomic propellant feed system designs for future aerospace vehicles.

  20. Solid Hydrogen Experiments for Atomic Propellants: Particle Formation Energy and Imaging Analyses

    Science.gov (United States)

    Palaszewski, Bryan

    2002-01-01

    This paper presents particle formation energy balances and detailed analyses of the images from experiments that were conducted on the formation of solid hydrogen particles in liquid helium during the Phase II testing in 2001. Solid particles of hydrogen were frozen in liquid helium and observed with a video camera. The solid hydrogen particle sizes and the total mass of hydrogen particles were estimated. The particle formation efficiency is also estimated. Particle sizes from the Phase I testing in 1999 and the Phase II testing in 2001 were similar. Though the 2001 testing created similar particles sizes, many new particle formation phenomena were observed. These experiment image analyses are one of the first steps toward visually characterizing these particles and it allows designers to understand what issues must be addressed in atomic propellant feed system designs for future aerospace vehicles.