WorldWideScience

Sample records for biological imaging system

  1. 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

  2. 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.

  3. Ion beam induced fluorescence imaging in biological systems

    International Nuclear Information System (INIS)

    Bettiol, Andrew A.; Mi, Zhaohong; Vanga, Sudheer Kumar; Chen, Ce-belle; Tao, Ye; Watt, Frank

    2015-01-01

    Imaging fluorescence generated by MeV ions in biological systems such as cells and tissue sections requires a high resolution beam (<100 nm), a sensitive detection system and a fluorescent probe that has a high quantum efficiency and low bleaching rate. For cutting edge applications in bioimaging, the fluorescence imaging technique needs to break the optical diffraction limit allowing for sub-cellular structure to be visualized, leading to a better understanding of cellular function. In a nuclear microprobe this resolution requirement can be readily achieved utilizing low beam current techniques such as Scanning Transmission Ion Microscopy (STIM). In recent times, we have been able to extend this capability to fluorescence imaging through the development of a new high efficiency fluorescence detection system, and through the use of new novel fluorescent probes that are resistant to ion beam damage (bleaching). In this paper we demonstrate ion beam induced fluorescence imaging in several biological samples, highlighting the advantages and challenges associated with using this technique

  4. Biological elements carry out optical tasks in coherent imaging systems

    Science.gov (United States)

    Ferraro, P.; Bianco, V.; Paturzo, M.; Miccio, L.; Memmolo, P.; Merola, F.; Marchesano, V.

    2016-03-01

    We show how biological elements, like live bacteria species and Red Blood Cells (RBCs) can accomplish optical functionalities in DH systems. Turbid media allow coherent microscopy despite the strong light scattering these provoke, acting on light just as moving diffusers. Furthermore, a turbid medium can have positive effects on a coherent imaging system, providing resolution enhancement and mimicking the action of noise decorrelation devices, thus yielding an image quality significantly higher than the quality achievable through a transparent medium in similar recording conditions. Besides, suspended RBCs are demonstrated to behave as controllable liquid micro-lenses, opening new possibilities in biophotonics for endoscopy imaging purposes, as well as telemedicine for point-of-care diagnostics in developing countries and low-resource settings.

  5. A photoacoustic tomography system for imaging of biological tissues

    International Nuclear Information System (INIS)

    Su Yixiong; Zhang Fan; Xu Kexin; Yao Jianquan; Wang, Ruikang K

    2005-01-01

    Non-invasive laser-induced photoacoustic tomography (PAT) is a promising imaging modality in the biomedical optical imaging field. This technology, based on the intrinsic optical properties of tissue and ultrasonic detection, overcomes the resolution disadvantage of pure-optical imaging caused by strong light scattering and the contrast and speckle disadvantages of pure ultrasonic imaging. Here, we report a PAT experimental system constructed in our laboratory. In our system, a Q-switched Nd : YAG pulse laser operated at 532 nm with a 8 ns pulse width is used to generate a photoacoustic signal. By using this system, the two-dimensional distribution of optical absorption in the tissue-mimicking phantom is reconstructed and has an excellent agreement with the original ones. The spatial resolution of the imaging system approaches 100 μm through about 4 cm of highly scattering medium

  6. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  7. Pseudorandom numbers: evolutionary models in image processing, biology, and nonlinear dynamic systems

    Science.gov (United States)

    Yaroslavsky, Leonid P.

    1996-11-01

    We show that one can treat pseudo-random generators, evolutionary models of texture images, iterative local adaptive filters for image restoration and enhancement and growth models in biology and material sciences in a unified way as special cases of dynamic systems with a nonlinear feedback.

  8. Imaging systems and algorithms to analyze biological samples in real-time using mobile phone microscopy.

    Science.gov (United States)

    Shanmugam, Akshaya; Usmani, Mohammad; Mayberry, Addison; Perkins, David L; Holcomb, Daniel E

    2018-01-01

    Miniaturized imaging devices have pushed the boundaries of point-of-care imaging, but existing mobile-phone-based imaging systems do not exploit the full potential of smart phones. This work demonstrates the use of simple imaging configurations to deliver superior image quality and the ability to handle a wide range of biological samples. Results presented in this work are from analysis of fluorescent beads under fluorescence imaging, as well as helminth eggs and freshwater mussel larvae under white light imaging. To demonstrate versatility of the systems, real time analysis and post-processing results of the sample count and sample size are presented in both still images and videos of flowing samples.

  9. A Checklist for Successful Quantitative Live Cell Imaging in Systems Biology

    Science.gov (United States)

    Sung, Myong-Hee

    2013-01-01

    Mathematical modeling of signaling and gene regulatory networks has provided unique insights about systems behaviors for many cell biological problems of medical importance. Quantitative single cell monitoring has a crucial role in advancing systems modeling of molecular networks. However, due to the multidisciplinary techniques that are necessary for adaptation of such systems biology approaches, dissemination to a wide research community has been relatively slow. In this essay, I focus on some technical aspects that are often under-appreciated, yet critical in harnessing live cell imaging methods to achieve single-cell-level understanding and quantitative modeling of molecular networks. The importance of these technical considerations will be elaborated with examples of successes and shortcomings. Future efforts will benefit by avoiding some pitfalls and by utilizing the lessons collectively learned from recent applications of imaging in systems biology. PMID:24709701

  10. Preclinical magnetic resonance imaging and systems biology in cancer research: current applications and challenges.

    Science.gov (United States)

    Albanese, Chris; Rodriguez, Olga C; VanMeter, John; Fricke, Stanley T; Rood, Brian R; Lee, YiChien; Wang, Sean S; Madhavan, Subha; Gusev, Yuriy; Petricoin, Emanuel F; Wang, Yue

    2013-02-01

    Biologically accurate mouse models of human cancer have become important tools for the study of human disease. The anatomical location of various target organs, such as brain, pancreas, and prostate, makes determination of disease status difficult. Imaging modalities, such as magnetic resonance imaging, can greatly enhance diagnosis, and longitudinal imaging of tumor progression is an important source of experimental data. Even in models where the tumors arise in areas that permit visual determination of tumorigenesis, longitudinal anatomical and functional imaging can enhance the scope of studies by facilitating the assessment of biological alterations, (such as changes in angiogenesis, metabolism, cellular invasion) as well as tissue perfusion and diffusion. One of the challenges in preclinical imaging is the development of infrastructural platforms required for integrating in vivo imaging and therapeutic response data with ex vivo pathological and molecular data using a more systems-based multiscale modeling approach. Further challenges exist in integrating these data for computational modeling to better understand the pathobiology of cancer and to better affect its cure. We review the current applications of preclinical imaging and discuss the implications of applying functional imaging to visualize cancer progression and treatment. Finally, we provide new data from an ongoing preclinical drug study demonstrating how multiscale modeling can lead to a more comprehensive understanding of cancer biology and therapy. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  11. A high-resolution optical imaging system for obtaining the serial transverse section images of biologic tissue

    Science.gov (United States)

    Wu, Li; Zhang, Bin; Wu, Ping; Liu, Qian; Gong, Hui

    2007-05-01

    A high-resolution optical imaging system was designed and developed to obtain the serial transverse section images of the biologic tissue, such as the mouse brain, in which new knife-edge imaging technology, high-speed and high-sensitive line-scan CCD and linear air bearing stages were adopted and incorporated with an OLYMPUS microscope. The section images on the tip of the knife-edge were synchronously captured by the reflection imaging in the microscope while cutting the biologic tissue. The biologic tissue can be sectioned at interval of 250 nm with the same resolution of the transverse section images obtained in x and y plane. And the cutting job can be automatically finished based on the control program wrote specially in advance, so we save the mass labor of the registration of the vast images data. In addition, by using this system a larger sample can be cut than conventional ultramicrotome so as to avoid the loss of the tissue structure information because of splitting the tissue sample to meet the size request of the ultramicrotome.

  12. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

  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. 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

  15. Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering.

    Directory of Open Access Journals (Sweden)

    Isaac Nuñez

    Full Text Available The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here

  16. Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering.

    Science.gov (United States)

    Nuñez, Isaac; Matute, Tamara; Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy; Federici, Fernán

    2017-01-01

    The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under

  17. 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.

  18. Development of a Portable 3CCD Camera System for Multispectral Imaging of Biological Samples

    Science.gov (United States)

    Lee, Hoyoung; Park, Soo Hyun; Noh, Sang Ha; Lim, Jongguk; Kim, Moon S.

    2014-01-01

    Recent studies have suggested the need for imaging devices capable of multispectral imaging beyond the visible region, to allow for quality and safety evaluations of agricultural commodities. Conventional multispectral imaging devices lack flexibility in spectral waveband selectivity for such applications. In this paper, a recently developed portable 3CCD camera with significant improvements over existing imaging devices is presented. A beam-splitter prism assembly for 3CCD was designed to accommodate three interference filters that can be easily changed for application-specific multispectral waveband selection in the 400 to 1000 nm region. We also designed and integrated electronic components on printed circuit boards with firmware programming, enabling parallel processing, synchronization, and independent control of the three CCD sensors, to ensure the transfer of data without significant delay or data loss due to buffering. The system can stream 30 frames (3-waveband images in each frame) per second. The potential utility of the 3CCD camera system was demonstrated in the laboratory for detecting defect spots on apples. PMID:25350510

  19. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  20. BETAview: a digital {beta}-imaging system for dynamic studies of biological phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Bertolucci, E.; Conti, M.; Mettivier, G.; Montesi, M.C. E-mail: montesi@na.infn.it; Russo, P

    2002-02-01

    We present a digital autoradiography (DAR) system, named BETAview, based on semiconductor pixel detectors and a single particle counting chip, for quantitative analysis of {beta}-emitting radioactive tracers in biological samples. The system is able to perform a real time monitoring of time-dependent biological phenomena. BETAview could be equipped either with GaAs or with Si semiconductor pixellated detectors. In this paper, we describe the results obtained with an assembly based on a Si detector, 300 {mu}m thick, segmented into 64x64 170 {mu}m size square pixels. The detector is bump-bonded to the low threshold, single particle counting chip named Medipix1, developed by a CERN-based European collaboration. The sensitive area is about 1 cm{sup 2}. Studies of background noise and detection efficiency have been performed. Moreover, time-resolved cellular uptake studies with radiolabelled molecules have been monitored. Specifically, we have followed in vivo and in real time, the [{sup 14}C]L-leucine amino acid uptake by eggs of Octopus vulgaris confirming the preliminary results of a previous paper. This opens the field of biomolecular kynetic studies with this new class of semiconductor DAR systems, whose evolution (using the Medipix2 chip, 256x256 pixels, 55 {mu}m pixel size) is soon to come.

  1. BETAview: a digital β-imaging system for dynamic studies of biological phenomena

    International Nuclear Information System (INIS)

    Bertolucci, E.; Conti, M.; Mettivier, G.; Montesi, M.C.; Russo, P.

    2002-01-01

    We present a digital autoradiography (DAR) system, named BETAview, based on semiconductor pixel detectors and a single particle counting chip, for quantitative analysis of β-emitting radioactive tracers in biological samples. The system is able to perform a real time monitoring of time-dependent biological phenomena. BETAview could be equipped either with GaAs or with Si semiconductor pixellated detectors. In this paper, we describe the results obtained with an assembly based on a Si detector, 300 μm thick, segmented into 64x64 170 μm size square pixels. The detector is bump-bonded to the low threshold, single particle counting chip named Medipix1, developed by a CERN-based European collaboration. The sensitive area is about 1 cm 2 . Studies of background noise and detection efficiency have been performed. Moreover, time-resolved cellular uptake studies with radiolabelled molecules have been monitored. Specifically, we have followed in vivo and in real time, the [ 14 C]L-leucine amino acid uptake by eggs of Octopus vulgaris confirming the preliminary results of a previous paper. This opens the field of biomolecular kynetic studies with this new class of semiconductor DAR systems, whose evolution (using the Medipix2 chip, 256x256 pixels, 55 μm pixel size) is soon to come

  2. Biological conversion system

    Science.gov (United States)

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  3. 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. © 2013 The Author Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

  4. Epithelial invasion outcompetes hypha development during Candida albicans infection as revealed by an image-based systems biology approach.

    Science.gov (United States)

    Mech, Franziska; Wilson, Duncan; Lehnert, Teresa; Hube, Bernhard; Thilo Figge, Marc

    2014-02-01

    Candida albicans is the most common opportunistic fungal pathogen of the human mucosal flora, frequently causing infections. The fungus is responsible for invasive infections in immunocompromised patients that can lead to sepsis. The yeast to hypha transition and invasion of host-tissue represent major determinants in the switch from benign colonizer to invasive pathogen. A comprehensive understanding of the infection process requires analyses at the quantitative level. Utilizing fluorescence microscopy with differential staining, we obtained images of C. albicans undergoing epithelial invasion during a time course of 6 h. An image-based systems biology approach, combining image analysis and mathematical modeling, was applied to quantify the kinetics of hyphae development, hyphal elongation, and epithelial invasion. The automated image analysis facilitates high-throughput screening and provided quantities that allow for the time-resolved characterization of the morphological and invasive state of fungal cells. The interpretation of these data was supported by two mathematical models, a kinetic growth model and a kinetic transition model, that were developed using differential equations. The kinetic growth model describes the increase in hyphal length and revealed that hyphae undergo mass invasion of epithelial cells following primary hypha formation. We also provide evidence that epithelial cells stimulate the production of secondary hyphae by C. albicans. Based on the kinetic transition model, the route of invasion was quantified in the state space of non-invasive and invasive fungal cells depending on their number of hyphae. This analysis revealed that the initiation of hyphae formation represents an ultimate commitment to invasive growth and suggests that in vivo, the yeast to hypha transition must be under exquisitely tight negative regulation to avoid the transition from commensal to pathogen invading the epithelium. © 2013 International Society for

  5. Microholographic imaging of biological samples

    International Nuclear Information System (INIS)

    Haddad, W.S.; Cullen, D.; Solem, J.C.; Longworth, J.W.; McPherson, A.; Boyer, K.; Rhodes, C.K.

    1990-01-01

    A camera system suitable for x-ray microholography has been constructed. Visible light Fourier transform microholograms of biological samples and other test targets have been recorded and reconstructed digitally using a glycerol microdrop as a reference wave source. Current results give a resolution of ∼4 - 10 λ with λ = 514.5 nm. 11 refs., 1 fig

  6. 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.

  7. Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture

    Science.gov (United States)

    Lassahn, Gordon D.; Lancaster, Gregory D.; Apel, William A.; Thompson, Vicki S.

    2013-01-08

    Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture are described. According to one embodiment, an image portion identification method includes accessing data regarding an image depicting a plurality of biological substrates corresponding to at least one biological sample and indicating presence of at least one biological indicator within the biological sample and, using processing circuitry, automatically identifying a portion of the image depicting one of the biological substrates but not others of the biological substrates.

  8. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

    Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

    2016-01-01

    Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

  9. Nutritional Systems Biology

    DEFF Research Database (Denmark)

    Jensen, Kasper

    and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

  10. Model system for plant cell biology: GFP imaging in living onion epidermal cells

    Science.gov (United States)

    Scott, A.; Wyatt, S.; Tsou, P. L.; Robertson, D.; Allen, N. S.

    1999-01-01

    The ability to visualize organelle localization and dynamics is very useful in studying cellular physiological events. Until recently, this has been accomplished using a variety of staining methods. However, staining can give inaccurate information due to nonspecific staining, diffusion of the stain or through toxic effects. The ability to target green fluorescent protein (GFP) to various organelles allows for specific labeling of organelles in vivo. The disadvantages of GFP thus far have been the time and money involved in developing stable transformants or maintaining cell cultures for transient expression. In this paper, we present a rapid transient expression system using onion epidermal peels. We have localized GFP to various cellular compartments (including the cell wall) to illustrate the utility of this method and to visualize dynamics of these compartments. The onion epidermis has large, living, transparent cells in a monolayer, making them ideal for visualizing GFP. This method is easy and inexpensive, and it allows for testing of new GFP fusion proteins in a living tissue to determine deleterious effects and the ability to express before stable transformants are attempted.

  11. Imaging system

    International Nuclear Information System (INIS)

    Froggatt, R.J.

    1981-01-01

    The invention provides a two dimensional imaging system in which a pattern of radiation falling on the system is detected to give electrical signals for each of a plurality of strips across the pattern. The detection is repeated for different orientations of the strips and the whole processed by compensated back projection. For a shadow x-ray system a plurality of strip x-ray detectors are rotated on a turntable. For lower frequencies the pattern may be rotated with a Dove prism and the strips condensed to suit smaller detectors with a cylindrical lens. (author)

  12. Imaging system

    International Nuclear Information System (INIS)

    Rushbrooke, J.G.; Ansorge, R.E.

    1987-01-01

    A moving object such as a container on a conveyor belt is imaged by an optical system onto a charge coupled device array in which the lines of the array are arranged perpendicular to the direction of motion of the object. The speed of movement of the object is sensed to generate electrical signals which are processed to provide shift signals enabling the shifting of data row to row in the array in synchronism with the movement of the container. The electrical charge associated with a given point on the array is transferred from one line to the other until it appears at the last line of the array, from which it is read out in known manner in conjunction with all other electrical charges associated with the row of charge coupled devices in the last line of the array. Due to the integrating effect achieved, the aperture of the imaging system can be much smaller than otherwise would be required, and/or the level of light illumination can be reduced. The imaging system can be applied to X-ray inspection devices, aerial surveillance or scanning of moving documents in copying processes. (author)

  13. Systems biology at work

    NARCIS (Netherlands)

    Martins Dos Santos, V.A.P.; Damborsky, J.

    2010-01-01

    In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now

  14. Plant Systems Biology (editorial)

    Science.gov (United States)

    In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

  15. Biophysics and systems biology.

    Science.gov (United States)

    Noble, Denis

    2010-03-13

    Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

  16. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

  17. 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 small animal organs, albeit at lower resolution (30,000 sampling points/image). In rodent models, imaging was performed using various fluorescent staining protocols including fluorescently labelled receptor ligands, labelled antibodies, FITC-dextrans, vital dyes and labelled cells administered topically or intravenously. Abdominal organs of large animals were accessed laparoscopically and contrasted using i.v. fluorescein-sodium. Articular cartilage 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

  18. Integrative radiation systems biology

    International Nuclear Information System (INIS)

    Unger, Kristian

    2014-01-01

    Maximisation of the ratio of normal tissue preservation and tumour cell reduction is the main concept of radiotherapy alone or combined with chemo-, immuno- or biologically targeted therapy. The foremost parameter influencing this ratio is radiation sensitivity and its modulation towards a more efficient killing of tumour cells and a better preservation of normal tissue at the same time is the overall aim of modern therapy schemas. Nevertheless, this requires a deep understanding of the molecular mechanisms of radiation sensitivity in order to identify its key players as potential therapeutic targets. Moreover, the success of conventional approaches that tried to statistically associate altered radiation sensitivity with any molecular phenotype such as gene expression proofed to be somewhat limited since the number of clinically used targets is rather sparse. However, currently a paradigm shift is taking place from pure frequentistic association analysis to the rather holistic systems biology approach that seeks to mathematically model the system to be investigated and to allow the prediction of an altered phenotype as the function of one single or a signature of biomarkers. Integrative systems biology also considers the data from different molecular levels such as the genome, transcriptome or proteome in order to partially or fully comprehend the causal chain of molecular mechanisms. An example for the application of this concept currently carried out at the Clinical Cooperation Group “Personalized Radiotherapy in Head and Neck Cancer” of the Helmholtz-Zentrum München and the LMU Munich is described. This review article strives for providing a compact overview on the state of the art of systems biology, its actual challenges, potential applications, chances and limitations in radiation oncology research working towards improved personalised therapy concepts using this relatively new methodology

  19. Logical analysis of biological systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian

    2005-01-01

    R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

  20. Biomarkers and Biological Spectral Imaging

    Science.gov (United States)

    2001-01-23

    G. Sowa, H. H. Mantsch, National Research Council Canada; S. L. Zhang, Unilever Research (USA) 85 Brain tissue charcterization using spectral imaging...image registration and of the expert staff of Hill Top Research in Winnipeg for hosting the hydration study. Financial assistance from Unilever Research

  1. Biological imaging in radiation therapy: role of positron emission tomography

    Energy Technology Data Exchange (ETDEWEB)

    Nestle, Ursula; Hentschel, Michael; Grosu, Anca-Ligia [Departments of Radiation Oncology, University of Freiburg, Robert Koch Str. 3, 79106 Freiburg (Germany); Weber, Wolfgang [Nuclear Medicine, University of Freiburg, Robert Koch Str. 3, 79106 Freiburg (Germany)], E-mail: ursula.nestle@uniklinik-freiburg.de

    2009-01-07

    In radiation therapy (RT), staging, treatment planning, monitoring and evaluation of response are traditionally based on computed tomography (CT) and magnetic resonance imaging (MRI). These radiological investigations have the significant advantage to show the anatomy with a high resolution, being also called anatomical imaging. In recent years, so called biological imaging methods which visualize metabolic pathways have been developed. These methods offer complementary imaging of various aspects of tumour biology. To date, the most prominent biological imaging system in use is positron emission tomography (PET), whose diagnostic properties have clinically been evaluated for years. The aim of this review is to discuss the valences and implications of PET in RT. We will focus our evaluation on the following topics: the role of biological imaging for tumour tissue detection/delineation of the gross tumour volume (GTV) and for the visualization of heterogeneous tumour biology. We will discuss the role of fluorodeoxyglucose-PET in lung and head and neck cancer and the impact of amino acids (AA)-PET in target volume delineation of brain gliomas. Furthermore, we summarize the data of the literature about tumour hypoxia and proliferation visualized by PET. We conclude that, regarding treatment planning in radiotherapy, PET offers advantages in terms of tumour delineation and the description of biological processes. However, to define the real impact of biological imaging on clinical outcome after radiotherapy, further experimental, clinical and cost/benefit analyses are required. (topical review)

  2. Biological imaging in radiation therapy: role of positron emission tomography.

    Science.gov (United States)

    Nestle, Ursula; Weber, Wolfgang; Hentschel, Michael; Grosu, Anca-Ligia

    2009-01-07

    In radiation therapy (RT), staging, treatment planning, monitoring and evaluation of response are traditionally based on computed tomography (CT) and magnetic resonance imaging (MRI). These radiological investigations have the significant advantage to show the anatomy with a high resolution, being also called anatomical imaging. In recent years, so called biological imaging methods which visualize metabolic pathways have been developed. These methods offer complementary imaging of various aspects of tumour biology. To date, the most prominent biological imaging system in use is positron emission tomography (PET), whose diagnostic properties have clinically been evaluated for years. The aim of this review is to discuss the valences and implications of PET in RT. We will focus our evaluation on the following topics: the role of biological imaging for tumour tissue detection/delineation of the gross tumour volume (GTV) and for the visualization of heterogeneous tumour biology. We will discuss the role of fluorodeoxyglucose-PET in lung and head and neck cancer and the impact of amino acids (AA)-PET in target volume delineation of brain gliomas. Furthermore, we summarize the data of the literature about tumour hypoxia and proliferation visualized by PET. We conclude that, regarding treatment planning in radiotherapy, PET offers advantages in terms of tumour delineation and the description of biological processes. However, to define the real impact of biological imaging on clinical outcome after radiotherapy, further experimental, clinical and cost/benefit analyses are required.

  3. Mammalian Synthetic Biology: Engineering Biological Systems.

    Science.gov (United States)

    Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

    2017-06-21

    The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

  4. Design and implementation of optical imaging and sensor systems for characterization of deep-sea biological camouflage

    Science.gov (United States)

    Haag, Justin Mathew

    The visual ecology of deep-sea animals has long been of scientific interest. In the open ocean, where there is no physical structure to hide within or behind, diverse strategies have evolved to solve the problem of camouflage from a potential predator. Simulations of specific predator-prey scenarios have yielded estimates of the range of possible appearances that an animal may exhibit. However, there is a limited amount of quantitative information available related to both animal appearance and the light field at mesopelagic depths (200 m to 1000 m). To mitigate this problem, novel optical instrumentation, taking advantage of recent technological advances, was developed and is described in this dissertation. In the first half of this dissertation, the appearance of mirrored marine animals is quantitatively evaluated. A portable optical imaging scatterometer was developed to measure angular reflectance, described by the bidirectional reflectance distribution function (BRDF), of biological specimens. The instrument allows for BRDF capture from samples of arbitrary size, over a significant fraction of the reflectance hemisphere. Multiple specimens representing two species of marine animals, collected at mesopelagic depths, were characterized using the scatterometer. Low-dimensional parametric models were developed to simplify use of the data sets, and to validate the BRDF method. Results from principal component analysis confirm that BRDF measurements can be used to study intra- and interspecific variability of mirrored marine animal appearance. Collaborative efforts utilizing the BRDF data sets to develop physically-based scattering models are underway. In the second half of this dissertation, another key part of the deep-sea biological camouflage problem is examined. Two underwater radiometers, capable of low-light measurements, were developed to address the lack of available information related to the deep-sea light field. Quantitative comparison of spectral

  5. Systems biology of fungal infection

    Directory of Open Access Journals (Sweden)

    Fabian eHorn

    2012-04-01

    Full Text Available Elucidation of pathogenicity mechanisms of the most important human pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections.A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviours in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions.We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modelling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.

  6. Electromagnetic fields in biological systems

    National Research Council Canada - National Science Library

    Lin, James C

    2012-01-01

    "Focusing on exposure, induced fields, and absorbed energy, this volume covers the interaction of electromagnetic fields and waves with biological systems, spanning static fields to terahertz waves...

  7. Medical Imaging System

    Science.gov (United States)

    1991-01-01

    The MD Image System, a true-color image processing system that serves as a diagnostic aid and tool for storage and distribution of images, was developed by Medical Image Management Systems, Huntsville, AL, as a "spinoff from a spinoff." The original spinoff, Geostar 8800, developed by Crystal Image Technologies, Huntsville, incorporates advanced UNIX versions of ELAS (developed by NASA's Earth Resources Laboratory for analysis of Landsat images) for general purpose image processing. The MD Image System is an application of this technology to a medical system that aids in the diagnosis of cancer, and can accept, store and analyze images from other sources such as Magnetic Resonance Imaging.

  8. 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...

  9. Excited states in biological systems

    International Nuclear Information System (INIS)

    Cilento, G.; Zinner, K.; Bechara, E.J.H.; Duran, N.; Baptista, R.C. de; Shimizu, Y.; Augusto, O.; Faljoni-Alario, A.; Vidigal, C.C.C.; Oliveira, O.M.M.F.; Haun, M.

    1979-01-01

    Some aspects of bioluminescence related to bioenergetics are discussed: 1. chemical generation of excited species, by means of two general processes: electron transference and cyclic - and linear peroxide cleavage; 2. biological systems capable of generating excited states and 3. biological functions of these states, specially the non-emissive ones (tripletes). The production and the role of non-emissive excited states in biological systems are analysed, the main purpose of the study being the search for non-emissive states. Experiences carried out in biological systems are described; results and conclusions are given. (M.A.) [pt

  10. Telemetry System of Biological Parameters

    Directory of Open Access Journals (Sweden)

    Jan Spisak

    2005-01-01

    Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

  11. Mapping biological systems to network systems

    CERN Document Server

    Rathore, Heena

    2016-01-01

    The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

  12. Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals.

    Science.gov (United States)

    Susaki, Etsuo A; Ueda, Hiroki R

    2016-01-21

    Organism-level systems biology aims to identify, analyze, control and design cellular circuits in organisms. Many experimental and computational approaches have been developed over the years to allow us to conduct these studies. Some of the most powerful methods are based on using optical imaging in combination with fluorescent labeling, and for those one of the long-standing stumbling blocks has been tissue opacity. Recently, the solutions to this problem have started to emerge based on whole-body and whole-organ clearing techniques that employ innovative tissue-clearing chemistry. Here, we review these advancements and discuss how combining new clearing techniques with high-performing fluorescent proteins or small molecule tags, rapid volume imaging and efficient image informatics is resulting in comprehensive and quantitative organ-wide, single-cell resolution experimental data. These technologies are starting to yield information on connectivity and dynamics in cellular circuits at unprecedented resolution, and bring us closer to system-level understanding of physiology and diseases of complex mammalian systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Static Analysis for Systems Biology

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

    2004-01-01

    This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

  14. Systems biology and medicine

    Indian Academy of Sciences (India)

    work could potentially provide us with ways to identify drug ... appropriately balance cause, effect, and context of a given clinical ... would not provide answers/solutions to multitude of tasks that were ... a major challenge of contemporary biology is to embark on an ... nificantly govern the life and responsiveness of cells.

  15. Quantum Effects in Biological Systems

    CERN Document Server

    2016-01-01

    Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

  16. Mechanics of bioinspired imaging systems

    Directory of Open Access Journals (Sweden)

    Zhengwei Li

    2016-01-01

    Full Text Available Imaging systems in nature have attracted a lot of research interest due to their superior optical and imaging characteristics. Recent advancements in materials science, mechanics, and stretchable electronics have led to successful development of bioinspired cameras that resemble the structures and functions of biological light-sensing organs. In this review, we discuss some recent progresses in mechanics of bioinspired imaging systems, including tunable hemispherical eyeball camera and artificial compound eye camera. The mechanics models and results reviewed in this article can provide efficient tools for design and optimization of such systems, as well as other related optoelectronic systems that combine rigid elements with soft substrates.

  17. Heuristic Strategies in Systems Biology

    Directory of Open Access Journals (Sweden)

    Fridolin Gross

    2016-06-01

    Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

  18. Scintillating Optical Fiber Imagers for biology

    International Nuclear Information System (INIS)

    Mastrippolito, R.

    1990-01-01

    S.O.F.I (Scintillating Optical Fiber Imager) is a detector developed to replace the autoradiographic films used in molecular biology for the location of radiolabelled ( 32 P) DNA molecules in blotting experiments. It analyses samples on a 25 x 25 cm 2 square area still 25 times faster than autoradiographic films, with a 1.75 and 3 mm resolution for two orthogonal directions. This device performs numerised images with a dynamic upper than 100 which allows the direct quantitation of the analysed samples. First, this thesis describes the S.O.F.I. development (Scintillating Optical Fibers, coding of these fibers and specific electronic for the treatment of the Multi-Anode Photo-Multiplier signals) and experiments made in collaboration with molecular biology laboratories. In a second place, we prove the feasibility of an automatic DNA sequencer issued from S.O.F.I [fr

  19. Histological image classification using biologically interpretable shape-based features

    International Nuclear Information System (INIS)

    Kothari, Sonal; Phan, John H; Young, Andrew N; Wang, May D

    2013-01-01

    Automatic cancer diagnostic systems based on histological image classification are important for improving therapeutic decisions. Previous studies propose textural and morphological features for such systems. These features capture patterns in histological images that are useful for both cancer grading and subtyping. However, because many of these features lack a clear biological interpretation, pathologists may be reluctant to adopt these features for clinical diagnosis. We examine the utility of biologically interpretable shape-based features for classification of histological renal tumor images. Using Fourier shape descriptors, we extract shape-based features that capture the distribution of stain-enhanced cellular and tissue structures in each image and evaluate these features using a multi-class prediction model. We compare the predictive performance of the shape-based diagnostic model to that of traditional models, i.e., using textural, morphological and topological features. The shape-based model, with an average accuracy of 77%, outperforms or complements traditional models. We identify the most informative shapes for each renal tumor subtype from the top-selected features. Results suggest that these shapes are not only accurate diagnostic features, but also correlate with known biological characteristics of renal tumors. Shape-based analysis of histological renal tumor images accurately classifies disease subtypes and reveals biologically insightful discriminatory features. This method for shape-based analysis can be extended to other histological datasets to aid pathologists in diagnostic and therapeutic decisions

  20. Compartmental study of biological systems

    International Nuclear Information System (INIS)

    Moretti, J.L.

    1975-01-01

    The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

  1. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...... to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many...

  2. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K

    2011-01-01

    to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

  3. Informing biological design by integration of systems and synthetic biology.

    Science.gov (United States)

    Smolke, Christina D; Silver, Pamela A

    2011-03-18

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. Development trend of radiation biology research-systems radiation biology

    International Nuclear Information System (INIS)

    Min Rui

    2010-01-01

    Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

  5. Imaging morphogenesis: technological advances and biological insights.

    Science.gov (United States)

    Keller, Philipp J

    2013-06-07

    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.

  6. 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.

  7. Medical imaging systems

    Science.gov (United States)

    Frangioni, John V

    2013-06-25

    A medical imaging system provides simultaneous rendering of visible light and diagnostic or functional images. The system may be portable, and may include adapters for connecting various light sources and cameras in open surgical environments or laparascopic or endoscopic environments. A user interface provides control over the functionality of the integrated imaging system. In one embodiment, the system provides a tool for surgical pathology.

  8. 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.

  9. Economic and biological costs of cardiac imaging

    Directory of Open Access Journals (Sweden)

    Picano Eugenio

    2005-05-01

    Full Text Available Abstract Medical imaging market consists of several billion tests per year worldwide. Out of these, at least one third are cardiovascular procedures. Keeping in mind that each test represents a cost, often a risk, and a diagnostic hypothesis, we can agree that every unnecessary and unjustifiable test is one test too many. Small individual costs, risks, and wastes multiplied by billions of examinations per year represent an important population, society and environmental burden. Unfortunately, the appropriateness of cardiac imaging is extra-ordinarily low and there is little awareness in patients and physicians of differential costs, radiological doses, and long term risks of different imaging modalities. For a resting cardiac imaging test, being the average cost (not charges of an echocardiogram equal to 1 (as a cost comparator, the cost of a CT is 3.1x, of a SPECT 3.27x, of a Cardiovascular Magnetic Resonance imaging 5.51x, of a PET 14.03x, and of a right and left heart catheterization 19.96x. For stress cardiac imaging, compared with the treadmill exercise test equal to 1 (as a cost comparator, the cost of stress echocardiography is 2.1x and of a stress SPECT scintigraphy is 5.7x. Biohazards and downstream long-term costs linked to radiation-induced oncogenesis should also be considered. The radiation exposure is absent in echo and magnetic resonance, and corresponds to 500 chest x rays for a sestamibi cardiac stress scan and to 1150 chest x rays for a thallium scan. The corresponding extra-risk in a lifetime of fatal cancer is 1 in 2000 exposed patients for a sestamibi stress and 1 in 1000 for a thallium scan. Increased awareness of economic, biologic, and environmental costs of cardiac imaging will hopefully lead to greater appropriateness, wisdom and prudence from both the prescriber and the practitioner. In this way, the sustainability of cardiac imaging will eventually improve.

  10. From systems biology to systems biomedicine.

    Science.gov (United States)

    Antony, Paul M A; Balling, Rudi; Vlassis, Nikos

    2012-08-01

    Systems Biology is about combining theory, technology, and targeted experiments in a way that drives not only data accumulation but knowledge as well. The challenge in Systems Biomedicine is to furthermore translate mechanistic insights in biological systems to clinical application, with the central aim of improving patients' quality of life. The challenge is to find theoretically well-chosen models for the contextually correct and intelligible representation of multi-scale biological systems. In this review, we discuss the current state of Systems Biology, highlight the emergence of Systems Biomedicine, and highlight some of the topics and views that we think are important for the efficient application of Systems Theory in Biomedicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Inverse problems in systems biology

    International Nuclear Information System (INIS)

    Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

    2009-01-01

    Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

  12. Nanoscale technology in biological systems

    CERN Document Server

    Greco, Ralph S; Smith, R Lane

    2004-01-01

    Reviewing recent accomplishments in the field of nanobiology Nanoscale Technology in Biological Systems introduces the application of nanoscale matrices to human biology. It focuses on the applications of nanotechnology fabrication to biomedical devices and discusses new physical methods for cell isolation and manipulation and intracellular communication at the molecular level. It also explores the application of nanobiology to cardiovascular diseases, oncology, transplantation, and a range of related disciplines. This book build a strong background in nanotechnology and nanobiology ideal for

  13. 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.

  14. Workshop Introduction: Systems Biology and Biological Models

    Science.gov (United States)

    As we consider the future of toxicity testing, the importance of applying biological models to this problem is clear. Modeling efforts exist along a continuum with respect to the level of organization (e.g. cell, tissue, organism) linked to the resolution of the model. Generally,...

  15. Systems biology approach to bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

    2012-06-01

    Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the ‘black box’.

  16. Systems biology: the reincarnation of systems theory applied in biology?

    Science.gov (United States)

    Wolkenhauer, O

    2001-09-01

    With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

  17. Tunable promoters in systems biology

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Petranovic, Dina; Jensen, Peter Ruhdal

    2005-01-01

    The construction of synthetic promoter libraries has represented a major breakthrough in systems biology, enabling the subtle tuning of enzyme activities. A number of tools are now available that allow the modulation of gene expression and the detection of changes in expression patterns. But, how...

  18. Systems Biology of Industrial Microorganisms

    Science.gov (United States)

    Papini, Marta; Salazar, Margarita; Nielsen, Jens

    The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

  19. Systems Biology-an interdisciplinary approach.

    Science.gov (United States)

    Friboulet, Alain; Thomas, Daniel

    2005-06-15

    System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

  20. Mathematical methods in systems biology.

    Science.gov (United States)

    Kashdan, Eugene; Duncan, Dominique; Parnell, Andrew; Schattler, Heinz

    2016-12-01

    The editors of this Special Issue of Mathematical Biosciences and Engineering were the organizers for the Third International Workshop "Mathematical Methods in System Biology" that took place on June 15-18, 2015 at the University College Dublin in Ireland. As stated in the workshop goals, we managed to attract a good mix of mathematicians and statisticians working on biological and medical applications with biologists and clinicians interested in presenting their challenging problems and looking to find mathematical and statistical tools for their solutions.

  1. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Bor-Sen Chen

    2013-10-01

    Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

  2. Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2013-01-01

    Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

  3. Carbon nanomaterials in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Pu Chun Ke [Laboratory of Single-Molecule Biophysics and Polymer Physics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634 (United States); Qiao Rui [Department of Mechanical Engineering, Clemson University, Clemson, SC 29634 (United States)

    2007-09-19

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  4. Systems Biology of the Fluxome

    Directory of Open Access Journals (Sweden)

    Miguel A. Aon

    2015-07-01

    Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

  5. Carbon nanomaterials in biological systems

    International Nuclear Information System (INIS)

    Pu Chun Ke; Qiao Rui

    2007-01-01

    This paper intends to reflect, from the biophysical viewpoint, our current understanding on interfacing nanomaterials, such as carbon nanotubes and fullerenes, with biological systems. Strategies for improving the solubility, and therefore, the bioavailability of nanomaterials in aqueous solutions are summarized. In particular, the underlining mechanisms of attaching biomacromolecules (DNA, RNA, proteins) and lysophospholipids onto carbon nanotubes and gallic acids onto fullerenes are analyzed. The diffusion and the cellular delivery of RNA-coated carbon nanotubes are characterized using fluorescence microscopy. The translocation of fullerenes across cell membranes is simulated using molecular dynamics to offer new insight into the complex issue of nanotoxicity. To assess the fate of nanomaterials in the environment, the biomodification of lipid-coated carbon nanotubes by the aquatic organism Daphnia magna is discussed. The aim of this paper is to illuminate the need for adopting multidisciplinary approaches in the field study of nanomaterials in biological systems and in the environment. (topical review)

  6. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

  7. Multipurpose Hyperspectral Imaging System

    Science.gov (United States)

    Mao, Chengye; Smith, David; Lanoue, Mark A.; Poole, Gavin H.; Heitschmidt, Jerry; Martinez, Luis; Windham, William A.; Lawrence, Kurt C.; Park, Bosoon

    2005-01-01

    A hyperspectral imaging system of high spectral and spatial resolution that incorporates several innovative features has been developed to incorporate a focal plane scanner (U.S. Patent 6,166,373). This feature enables the system to be used for both airborne/spaceborne and laboratory hyperspectral imaging with or without relative movement of the imaging system, and it can be used to scan a target of any size as long as the target can be imaged at the focal plane; for example, automated inspection of food items and identification of single-celled organisms. The spectral resolution of this system is greater than that of prior terrestrial multispectral imaging systems. Moreover, unlike prior high-spectral resolution airborne and spaceborne hyperspectral imaging systems, this system does not rely on relative movement of the target and the imaging system to sweep an imaging line across a scene. This compact system (see figure) consists of a front objective mounted at a translation stage with a motorized actuator, and a line-slit imaging spectrograph mounted within a rotary assembly with a rear adaptor to a charged-coupled-device (CCD) camera. Push-broom scanning is carried out by the motorized actuator which can be controlled either manually by an operator or automatically by a computer to drive the line-slit across an image at a focal plane of the front objective. To reduce the cost, the system has been designed to integrate as many as possible off-the-shelf components including the CCD camera and spectrograph. The system has achieved high spectral and spatial resolutions by using a high-quality CCD camera, spectrograph, and front objective lens. Fixtures for attachment of the system to a microscope (U.S. Patent 6,495,818 B1) make it possible to acquire multispectral images of single cells and other microscopic objects.

  8. Biological Potential in Serpentinizing Systems

    Science.gov (United States)

    Hoehler, Tori M.

    2016-01-01

    Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

  9. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  10. Anion binding in biological systems

    International Nuclear Information System (INIS)

    Feiters, Martin C; Meyer-Klaucke, Wolfram; Kostenko, Alexander V; Soldatov, Alexander V; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Kuepper, Frithjof C; Hollenstein, Kaspar; Locher, Kaspar P; Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R

    2009-01-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L 3 (2p 3/2 ) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  11. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  12. Nonlinear dynamics in biological systems

    CERN Document Server

    Carballido-Landeira, Jorge

    2016-01-01

    This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

  13. Medical imaging systems

    Science.gov (United States)

    Frangioni, John V [Wayland, MA

    2012-07-24

    A medical imaging system provides simultaneous rendering of visible light and fluorescent images. The system may employ dyes in a small-molecule form that remains in a subject's blood stream for several minutes, allowing real-time imaging of the subject's circulatory system superimposed upon a conventional, visible light image of the subject. The system may also employ dyes or other fluorescent substances associated with antibodies, antibody fragments, or ligands that accumulate within a region of diagnostic significance. In one embodiment, the system provides an excitation light source to excite the fluorescent substance and a visible light source for general illumination within the same optical guide that is used to capture images. In another embodiment, the system is configured for use in open surgical procedures by providing an operating area that is closed to ambient light. More broadly, the systems described herein may be used in imaging applications where a visible light image may be usefully supplemented by an image formed from fluorescent emissions from a fluorescent substance that marks areas of functional interest.

  14. 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.

  15. 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.

  16. [Network structures in biological systems].

    Science.gov (United States)

    Oleskin, A V

    2013-01-01

    Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

  17. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  18. Systems biology and biomarker discovery

    Energy Technology Data Exchange (ETDEWEB)

    Rodland, Karin D.

    2010-12-01

    Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

  19. Radical production in biological systems

    International Nuclear Information System (INIS)

    Johnson, J.R.; Akabani, G.

    1994-10-01

    This paper describes our effort to develop a metric for radiation exposure that is more fundamental than adsorbed dose and upon which a metric for exposure to chemicals could be based. This metric is based on the production of radicals by the two agents. Radicals produced by radiation in biological systems commonly assumed to be the same as those produced in water despite the presence of a variety of complex molecules. This may explain why the extensive efforts to describe the relationship between energy deposition (track structure) and molecular damage to DNA, based on the spectrum of radicals produced, have not been successful in explaining simple biological effects such as cell killing. Current models assume that DNA and its basic elements are immersed in water-like media and only model the production and diffusion of water-based radicals and their interaction with DNA structures; these models lack the cross sections associated with each macro-component of DNA and only treat water-based radicals. It has been found that such models are not realistic because DNA is not immersed in pure water. A computer code capable of simulating electron tracks, low-energy electrons, energy deposition in small molecules, and radical production and diffusion in water like media has been developed. This code is still in at a primitive stage and development is continuing. It is being used to study radical production by radiation, and radical diffusion and interactions in simple molecular systems following their production. We are extending the code to radical production by chemicals to complement our PBPK modeling efforts. It therefore has been developed primarily for use with radionuclides that are in biological materials, and not for radiation fields

  20. Quantitative luminescence imaging system

    Science.gov (United States)

    Erwin, David N.; Kiel, Johnathan L.; Batishko, Charles R.; Stahl, Kurt A.

    1990-01-01

    The QLIS images and quantifies low-level chemiluminescent reactions in an electromagnetic field. It is capable of real time nonperturbing measurement and simultaneous recording of many biochemical and chemical reactions such as luminescent immunoassays or enzyme assays. The system comprises image transfer optics, a low-light level digitizing camera with image intensifying microchannel plates, an image process or, and a control computer. The image transfer optics may be a fiber image guide with a bend, or a microscope, to take the light outside of the RF field. Output of the camera is transformed into a localized rate of cumulative digitalized data or enhanced video display or hard-copy images. The system may be used as a luminescent microdosimetry device for radiofrequency or microwave radiation, as a thermal dosimeter, or in the dosimetry of ultra-sound (sonoluminescence) or ionizing radiation. It provides a near-real-time system capable of measuring the extremely low light levels from luminescent reactions in electromagnetic fields in the areas of chemiluminescence assays and thermal microdosimetry, and is capable of near-real-time imaging of the sample to allow spatial distribution analysis of the reaction. It can be used to instrument three distinctly different irradiation configurations, comprising (1) RF waveguide irradiation of a small Petri-dish-shaped sample cell, (2) RF irradiation of samples in a microscope for the microscopie imaging and measurement, and (3) RF irradiation of small to human body-sized samples in an anechoic chamber.

  1. Imaging of Biological Tissues by Visible Light CDI

    Science.gov (United States)

    Karpov, Dmitry; Dos Santos Rolo, Tomy; Rich, Hannah; Fohtung, Edwin

    Recent advances in the use of synchrotron and X-ray free electron laser (XFEL) based coherent diffraction imaging (CDI) with application to material sciences and medicine proved the technique to be efficient in recovering information about the samples encoded in the phase domain. The current state-of-the-art algorithms of reconstruction are transferable to optical frequencies, which makes laser sources a reasonable milestone both in technique development and applications. Here we present first results from table-top laser CDI system for imaging of biological tissues and reconstruction algorithms development and discuss approaches that are complimenting the data quality improvement that is applicable to visible light frequencies due to it's properties. We demonstrate applicability of the developed methodology to a wide class of soft bio-matter and condensed matter systems. This project is funded by DOD-AFOSR under Award No FA9550-14-1-0363 and the LANSCE Professorship at LANL.

  2. Integrating phosphoproteomics in systems biology

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2014-07-01

    Full Text Available Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed.

  3. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  4. Magnetoacoustic Imaging of Electrical Conductivity of Biological Tissues at a Spatial Resolution Better than 2 mm

    OpenAIRE

    Hu, Gang; He, Bin

    2011-01-01

    Magnetoacoustic tomography with magnetic induction (MAT-MI) is an emerging approach for noninvasively imaging electrical impedance properties of biological tissues. The MAT-MI imaging system measures ultrasound waves generated by the Lorentz force, having been induced by magnetic stimulation, which is related to the electrical conductivity distribution in tissue samples. MAT-MI promises to provide fine spatial resolution for biological tissue imaging as compared to ultrasound resolution. In t...

  5. Institute for Genomics and Systems Biology

    Science.gov (United States)

    Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

  6. Answering biological questions: Querying a systems biology database for nutrigenomics

    NARCIS (Netherlands)

    Evelo, C.T.; Bochove, K. van; Saito, J.T.

    2011-01-01

    The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

  7. Imaging with PET system

    International Nuclear Information System (INIS)

    Das, B.K.; Noreen Norfaraheen Lee Abdullah

    2012-01-01

    PET deals with biochemistry and metabolic changes that occur at molecular level. Hence, PET differs fundamentally from other imaging modalities. CT imaging is based on tissue density, whereas MRI conveys anatomic information based on proton density and proton relaxation dynamics. CT and MRI are useful in clinical diagnosis only when disease process has caused significant anatomic alterations. However, in most disease conditions chemical changes precede anatomic changes, that can be detected by PET technology. Thus, PET can provide earliest and unique information about ongoing disease process long before anatomic or structural changes take place. There is no other modality available at present that can replace PET technology. Although PET produces cross-sectional images like that obtained in MRI or CT, they represent circulation, function and metabolism, and not anatomic structure. PET is extremely sensitive measuring quantitatively concentration of tracers in nano to pico-molar range. Thus, PET enables merger of biochemistry and biology in medicine giving birth to molecular medicine that focuses on identifying the molecular errors of disease leading to developing molecular corrections including gene therapy. Molecular imaging with PET has been playing a role in examining the biological nature of a disease condition and its characterization to guide selection and evaluation of treatment. (author)

  8. Raster images vectorization system

    OpenAIRE

    Genytė, Jurgita

    2006-01-01

    The problem of raster images vectorization was analyzed and researched in this work. Existing vectorization systems are quite expensive, the results are inaccurate, and the manual vectorization of a large number of drafts is impossible. That‘s why our goal was to design and develop a new raster images vectorization system using our suggested automatic vectorization algorithm and the way to record results in a new universal vectorial file format. The work consists of these main parts: analysis...

  9. Imaging and the new biology: What's wrong with this picture?

    Science.gov (United States)

    Vannier, Michael W.

    2004-05-01

    The Human Genome has been defined, giving us one part of the equation that stems from the central dogma of molecular biology. Despite this awesome scientific achievement, the correspondence between genomics and imaging is weak, since we cannot predict an organism's phenotype from even perfect knowledge of its genetic complement. Biological knowledge comes in several forms, and the genome is perhaps the best known and most completely understood type. Imaging creates another form of biological information, providing the ability to study morphology, growth and development, metabolic processes, and diseases in vitro and in vivo at many levels of scale. The principal challenge in biomedical imaging for the future lies in the need to reconcile the data provided by one or multiple modalities with other forms of biological knowledge, most importantly the genome, proteome, physiome, and other "-ome's." To date, the imaging science community has not set a high priority on the unification of their results with genomics, proteomics, and physiological functions in most published work. Images are relatively isolated from other forms of biological data, impairing our ability to conceive and address many fundamental questions in research and clinical practice. This presentation will explain the challenge of biological knowledge integration in basic research and clinical applications from the standpoint of imaging and image processing. The impediments to progress, isolation of the imaging community, and mainstream of new and future biological science will be identified, so the critical and immediate need for change can be highlighted.

  10. Improved image alignment method in application to X-ray images and biological images.

    Science.gov (United States)

    Wang, Ching-Wei; Chen, Hsiang-Chou

    2013-08-01

    Alignment of medical images is a vital component of a large number of applications throughout the clinical track of events; not only within clinical diagnostic settings, but prominently so in the area of planning, consummation and evaluation of surgical and radiotherapeutical procedures. However, image registration of medical images is challenging because of variations on data appearance, imaging artifacts and complex data deformation problems. Hence, the aim of this study is to develop a robust image alignment method for medical images. An improved image registration method is proposed, and the method is evaluated with two types of medical data, including biological microscopic tissue images and dental X-ray images and compared with five state-of-the-art image registration techniques. The experimental results show that the presented method consistently performs well on both types of medical images, achieving 88.44 and 88.93% averaged registration accuracies for biological tissue images and X-ray images, respectively, and outperforms the benchmark methods. Based on the Tukey's honestly significant difference test and Fisher's least square difference test tests, the presented method performs significantly better than all existing methods (P ≤ 0.001) for tissue image alignment, and for the X-ray image registration, the proposed method performs significantly better than the two benchmark b-spline approaches (P < 0.001). The software implementation of the presented method and the data used in this study are made publicly available for scientific communities to use (http://www-o.ntust.edu.tw/∼cweiwang/ImprovedImageRegistration/). cweiwang@mail.ntust.edu.tw.

  11. Fostering synergy between cell biology and systems biology.

    Science.gov (United States)

    Eddy, James A; Funk, Cory C; Price, Nathan D

    2015-08-01

    In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  12. Quantum Dynamics in Biological Systems

    Science.gov (United States)

    Shim, Sangwoo

    In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

  13. Editorial overview : Systems biology for biotechnology

    NARCIS (Netherlands)

    Heinemann, Matthias; Pilpel, Yitzhak

    About 15 years ago, systems biology was introduced as a novel approach to biological research. On the one side, its introduction was a result of the recognition that through solely the reductionist approach, we would ulti- mately not be able to understand how biological systems function as a whole.

  14. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

    2011-08-11

    Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

  15. Adaptable data management for systems biology investigations

    Directory of Open Access Journals (Sweden)

    Burdick David

    2009-03-01

    Full Text Available Abstract Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. Results The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry. We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Conclusion Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

  16. Magnetic Actuation of Biological Systems

    Science.gov (United States)

    Lauback, Stephanie D.

    Central to the advancement of many biomedical and nanotechnology capabilities is the capacity to precisely control the motion of micro and nanostructures. These applications range from single molecule experiments to cell isolation and separation, to drug delivery and nanomachine manipulation. This dissertation focuses on actuation of biological micro- and nano-entities through the use of weak external magnetic fields, superparamagnetic beads, and ferromagnetic thin films. The magnetic platform presents an excellent method for actuation of biological systems due to its ability to directly control the motion of an array of micro and nanostructures in real-time with calibrated picoNewton forces. The energy landscape of two ferromagnetic thin film patterns (disks and zigzag wires) is experimentally explored and compared to corresponding theoretical models to quantify the applied forces and trajectories of superparamagnetic beads due to the magnetic traps. A magnetic method to directly actuate DNA nanomachines in real-time with nanometer resolution and sub-second response times using micromagnetic control was implemented through the use of stiff DNA micro-levers which bridged the large length scale mismatch between the micro-actuator and the nanomachine. Compared to current alternative methods which are limited in the actuation speeds and the number of reconfiguration states of DNA constructs, this magnetic approach enables fast actuation (˜ milliseconds) and reconfigurable conformations achieved through a continuous range of finely tuned steps. The system was initially tested through actuation of the stiff arm tethered to the surface, and two prototype DNA nanomachines (rotor and hinge) were successfully actuated using the stiff mechanical lever. These results open new possibilities in the development of functional robotic systems at the molecular scale. In exploiting the use of DNA stiff levers, a new technique was also developed to investigate the emergence of the

  17. Scorpion image segmentation system

    Science.gov (United States)

    Joseph, E.; Aibinu, A. M.; Sadiq, B. A.; Bello Salau, H.; Salami, M. J. E.

    2013-12-01

    Death as a result of scorpion sting has been a major public health problem in developing countries. Despite the high rate of death as a result of scorpion sting, little report exists in literature of intelligent device and system for automatic detection of scorpion. This paper proposed a digital image processing approach based on the floresencing characteristics of Scorpion under Ultra-violet (UV) light for automatic detection and identification of scorpion. The acquired UV-based images undergo pre-processing to equalize uneven illumination and colour space channel separation. The extracted channels are then segmented into two non-overlapping classes. It has been observed that simple thresholding of the green channel of the acquired RGB UV-based image is sufficient for segmenting Scorpion from other background components in the acquired image. Two approaches to image segmentation have also been proposed in this work, namely, the simple average segmentation technique and K-means image segmentation. The proposed algorithm has been tested on over 40 UV scorpion images obtained from different part of the world and results obtained show an average accuracy of 97.7% in correctly classifying the pixel into two non-overlapping clusters. The proposed 1system will eliminate the problem associated with some of the existing manual approaches presently in use for scorpion detection.

  18. Stochastic chemical kinetics theory and (mostly) systems biological applications

    CERN Document Server

    Érdi, Péter; Lente, Gabor

    2014-01-01

    This volume reviews the theory and simulation methods of stochastic kinetics by integrating historical and recent perspectives, presents applications, mostly in the context of systems biology and also in combustion theory. In recent years, due to the development in experimental techniques, such as optical imaging, single cell analysis, and fluorescence spectroscopy, biochemical kinetic data inside single living cells have increasingly been available. The emergence of systems biology brought renaissance in the application of stochastic kinetic methods.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

    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 response to radiation therapy (15.5 Gy) was assessed with micro-CT. Results: The tumor volume measured with free-breathing micro-CT scans was greater than the volume calculated by histology. Nevertheless, this imaging approach demonstrated that lung cancers with mutant p53 grew more rapidly than lung tumors with wild-type p53 and also showed that radiation therapy increased the doubling time of p53 mutant lung cancers fivefold. Conclusions: Micro-CT is an effective tool to noninvasively measure the growth of primary lung cancers in genetically engineered mice and assess tumor response to radiation therapy. This imaging approach will be useful to study the radiation biology of lung cancer.

  20. Applicability of Computational Systems Biology in Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning; Hadrup, Niels; Audouze, Karine Marie Laure

    2014-01-01

    be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method......Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources...... and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search...

  1. Strategies for Biologic Image-Guided Dose Escalation: A Review

    International Nuclear Information System (INIS)

    Sovik, Aste; Malinen, Eirik; Olsen, Dag Rune

    2009-01-01

    There is increasing interest in how to incorporate functional and molecular information obtained by noninvasive, three-dimensional tumor imaging into radiotherapy. The key issues are to identify radioresistant regions that can be targeted for dose escalation, and to develop radiation dose prescription and delivery strategies providing optimal treatment for the individual patient. In the present work, we review the proposed strategies for biologic image-guided dose escalation with intensity-modulated radiation therapy. Biologic imaging modalities and the derived images are discussed, as are methods for target volume delineation. Different dose escalation strategies and techniques for treatment delivery and treatment plan evaluation are also addressed. Furthermore, we consider the need for response monitoring during treatment. We conclude with a summary of the current status of biologic image-based dose escalation and of areas where further work is needed for this strategy to become incorporated into clinical practice

  2. Metabolomics: Definitions and Significance in Systems Biology.

    Science.gov (United States)

    Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

    2017-01-01

    Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

  3. Systems biology of personalized nutrition

    NARCIS (Netherlands)

    Ommen, B. van; Broek, T. van den; Hoogh, I. de; Erk, M. van; Someren, E. van; Rouhani-Rankouhi, T.; Anthony, J.C.; Hogenelst, K.; Pasman, W.; Boorsma, A.; Wopereis, S.

    2017-01-01

    Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the

  4. Fiji: an open-source platform for biological-image analysis.

    Science.gov (United States)

    Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

    2012-06-28

    Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

  5. Introduction to basic molecular biologic techniques for molecular imaging researches

    International Nuclear Information System (INIS)

    Kang, Joo Hyun

    2004-01-01

    Molecular imaging is a rapidly growing field due to the advances in molecular biology and imaging technologies. With the introduction of imaging reporter genes into the cell, diverse cellular processes can be monitored, quantified and imaged non-invasively in vivo. These processes include the gene expression, protein-protein interactions, signal transduction pathways, and monitoring of cells such as cancer cells, immune cells, and stem cells. In the near future, molecular imaging analysis will allow us to observe the incipience and progression of the disease. These will make us easier to give a diagnosis in the early stage of intractable diseases such as cancer, neuro-degenerative disease, and immunological disorders. Additionally, molecular imaging method will be a valuable tool for the real-time evaluation of cells in molecular biology and the basic biological studies. As newer and more powerful molecular imaging tools become available, it will be necessary to corporate clinicians, molecular biologists and biochemists for the planning, interpretation, and application of these techniques to their fullest potential. In order for such a multidisciplinary team to be effective, it is essential that a common understanding of basic biochemical and molecular biologic techniques is achieved. Basic molecular techniques for molecular imaging methods are presented in this paper

  6. Philosophy of Systems and Synthetic Biology

    DEFF Research Database (Denmark)

    Green, Sara

    2017-01-01

    This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

  7. Automated force volume image processing for biological samples.

    Directory of Open Access Journals (Sweden)

    Pavel Polyakov

    2011-04-01

    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.

  8. Nuclear imaging system

    International Nuclear Information System (INIS)

    Barrett, H.H.; Horrigan, F.A.

    1975-01-01

    This invention relates to a nuclear imaging system for mapping the source of high energy nuclear particles from a living organ which has selectively absorbed a radioactive compound by spatially coding the energy from the source in a Fresnel pattern on a detector and decoding the detector output to prouce an image of the source. The coding is produced by a Fresnel zone plate interposed between the nuclear energy source and the detector whose position is adjustable with respect to the detector to focus the slices of the nuclear source on the detector. By adjusting the zone plate to a plurality of positions, data from a plurality of cross-sectional slices are produced from which a three-dimensional image of the nuclear source may be obtained. (Patent Office Record)

  9. Micro-separation toward systems biology.

    Science.gov (United States)

    Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

    2006-02-17

    Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

  10. Biological Systems Thinking for Control Engineering Design

    Directory of Open Access Journals (Sweden)

    D. J. Murray-Smith

    2004-01-01

    Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

  11. Impact of Thermodynamic Principles in Systems Biology

    NARCIS (Netherlands)

    Heijnen, J.J.

    2010-01-01

    It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

  12. Aspergilli: Systems biology and industrial applications

    DEFF Research Database (Denmark)

    Knuf, Christoph; Nielsen, Jens

    2012-01-01

    possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

  13. Radiographic imaging system

    International Nuclear Information System (INIS)

    Davis, L. Jr.; Barrett, H.H.

    1979-01-01

    This invention describes a system for imaging a subject, such as a human being, in which there has been injected a contrast agent which absorbs radiation of a predetermined frequency. The system utilizes a source of high energy radiation such as X or gamma radiation. The source is a composite of first and second radiating materials each of which is arranged in a predetermined pattern or code, each pattern having both luminous and dark regions. In one embodiment, the luminous regions of one pattern are in registration with the dark regions of the other pattern, these regions being spaced apart in an alternative embodiment. The characteristic frequencies of radiation emitted by the first and second materials are respectively lower and higher than the predetermined absorption frequency. A detector of radiation is positioned relative to the subject and the source such that radiation propagating through the subject is incident upon the detector. Since the absorption edge of the contrast agent lies between the two characteristic frequencies of radiation, radiation from the second material is preferentially absorbed by the contrast agent with the result that the contrast agent appears to be illuminated by a coded source while the remainder of the subject may be regarded as illuminated essentially by a uniform uncoded source. Imaging is accomplished by a decoding of a detected coded image. Substances within the subject having other absorption frequencies are not imaged since the radiations of both materials are essentially equally absorbed by the subject so that the source appears uncoded

  14. Systems biology in critical-care nursing.

    Science.gov (United States)

    Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

    2011-01-01

    Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

  15. Marine biological data and information management system

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.

    Indian National Oceanographic Data Centre (INODC) is engaged in developing a marine biological data and information management system (BIODIMS). This system will contain the information on zooplankton in the water column, zoobenthic biomass...

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

    Science.gov (United States)

    Catapano, Ilaria; Soldovieri, Francesco

    2016-04-01

    Devices exploiting waves in the frequency range from 0.1 THz to 10 THz (corresponding to a free-space wavelength ranging from 30 μm to 3 mm) deserve attention as diagnostic technologies for cultural heritage. THz waves are, indeed, non-ionizing radiations capable of penetrating into non-metallic materials, which are opaque to both visible and infrared waves, without implying long term risks to the molecular stability of the exposed objects and humans. Moreover, THz surveys involve low poewr probing waves, are performed without contact with the object and, thanks to the recent developments, which have allowed the commercialization of compact, flexible and portable systems, maybe performed in loco (i.e. in the place where the artworks are usually located). On the other hand, THz devices can be considered as the youngest among the sensing and imaging electromagnetic techniques and their actual potentialities in terms of characterization of artworks is an ongoing research activity. As a contribution within this context, we have performed time of flight THz imaging [1,2] on ceramic and marble objects. In particular, we surveyed majolica tiles produced by Neapolitan ceramists in the 18th and 19th centuries with the aim to gather information on their structure, constructive technique and conservation state. Moreover, we investigated a Marmo di Candoglia fragment in order to characterize the biological attach affecting it. All the surveys were carried out by using the Fiber-Coupled Terahertz Time Domain System (FICO) developed by Z-Omega and available at the Institute of Electromagnetic Sensing of the Environment (IREA). This system is equipped with fiber optic coupled transmitting and receiving probes and with an automatic positioning system enabling to scan a 150 mm x 150 mm area under a reflection measurement configuration. Based on the obtained results we can state that the use of THz waves allows: - the reconstruction of the object topography; - the geometrical

  17. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  18. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  19. Genomes, Phylogeny, and Evolutionary Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  20. Quantitative mass imaging of single biological macromolecules.

    Science.gov (United States)

    Young, Gavin; Hundt, Nikolas; Cole, Daniel; Fineberg, Adam; Andrecka, Joanna; Tyler, Andrew; Olerinyova, Anna; Ansari, Ayla; Marklund, Erik G; Collier, Miranda P; Chandler, Shane A; Tkachenko, Olga; Allen, Joel; Crispin, Max; Billington, Neil; Takagi, Yasuharu; Sellers, James R; Eichmann, Cédric; Selenko, Philipp; Frey, Lukas; Riek, Roland; Galpin, Martin R; Struwe, Weston B; Benesch, Justin L P; Kukura, Philipp

    2018-04-27

    The cellular processes underpinning life are orchestrated by proteins and their interactions. The associated structural and dynamic heterogeneity, despite being key to function, poses a fundamental challenge to existing analytical and structural methodologies. We used interferometric scattering microscopy to quantify the mass of single biomolecules in solution with 2% sequence mass accuracy, up to 19-kilodalton resolution, and 1-kilodalton precision. We resolved oligomeric distributions at high dynamic range, detected small-molecule binding, and mass-imaged proteins with associated lipids and sugars. These capabilities enabled us to characterize the molecular dynamics of processes as diverse as glycoprotein cross-linking, amyloidogenic protein aggregation, and actin polymerization. Interferometric scattering mass spectrometry allows spatiotemporally resolved measurement of a broad range of biomolecular interactions, one molecule at a time. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  1. Towards multidimensional radiotherapy (MD-CRT): biological imaging and biological conformality

    International Nuclear Information System (INIS)

    Ling, C. Clifton; Humm, John; Larson, Steven; Amols, Howard; Fuks, Zvi; Leibel, Steven; Koutcher, Jason A.

    2000-01-01

    Purpose: The goals of this study were to survey and summarize the advances in imaging that have potential applications in radiation oncology, and to explore the concept of integrating physical and biological conformality in multidimensional conformal radiotherapy (MD-CRT). Methods and Materials: The advances in three-dimensional conformal radiotherapy (3D-CRT) have greatly improved the physical conformality of treatment planning and delivery. The development of intensity-modulated radiotherapy (IMRT) has provided the 'dose painting' or 'dose sculpting' ability to further customize the delivered dose distribution. The improved capabilities of nuclear magnetic resonance imaging and spectroscopy, and of positron emission tomography, are beginning to provide physiological and functional information about the tumor and its surroundings. In addition, molecular imaging promises to reveal tumor biology at the genotype and phenotype level. These developments converge to provide significant opportunities for enhancing the success of radiotherapy. Results: The ability of IMRT to deliver nonuniform dose patterns by design brings to fore the question of how to 'dose paint' and 'dose sculpt', leading to the suggestion that 'biological' images may be of assistance. In contrast to the conventional radiological images that primarily provide anatomical information, biological images reveal metabolic, functional, physiological, genotypic, and phenotypic data. Important for radiotherapy, the new and noninvasive imaging methods may yield three-dimensional radiobiological information. Studies are urgently needed to identify genotypes and phenotypes that affect radiosensitivity, and to devise methods to image them noninvasively. Incremental to the concept of gross, clinical, and planning target volumes (GTV, CTV, and PTV), we propose the concept of 'biological target volume' (BTV) and hypothesize that BTV can be derived from biological images and that their use may incrementally improve

  2. Heart Imaging System

    Science.gov (United States)

    1993-01-01

    Johnson Space Flight Center's device to test astronauts' heart function in microgravity has led to the MultiWire Gamma Camera, which images heart conditions six times faster than conventional devices. Dr. Jeffrey Lacy, who developed the technology as a NASA researcher, later formed Proportional Technologies, Inc. to develop a commercially viable process that would enable use of Tantalum-178 (Ta-178), a radio-pharmaceutical. His company supplies the generator for the radioactive Ta-178 to Xenos Medical Systems, which markets the camera. Ta-178 can only be optimally imaged with the camera. Because the body is subjected to it for only nine minutes, the radiation dose is significantly reduced and the technique can be used more frequently. Ta-178 also enables the camera to be used on pediatric patients who are rarely studied with conventional isotopes because of the high radiation dosage.

  3. Genome Scale Modeling in Systems Biology: Algorithms and Resources

    Science.gov (United States)

    Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

    2014-01-01

    In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

  4. An engineering design approach to systems biology.

    Science.gov (United States)

    Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

    2017-07-17

    Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

  5. Drawing inspiration from biological optical systems

    Science.gov (United States)

    Wolpert, H. D.

    2009-08-01

    Bio-Mimicking/Bio-Inspiration: How can we not be inspired by Nature? Life has evolved on earth over the last 3.5 to 4 billion years. Materials formed during this time were not toxic; they were created at low temperatures and low pressures unlike many of the materials developed today. The natural materials formed are self-assembled, multifunctional, nonlinear, complex, adaptive, self-repairing and biodegradable. The designs that failed are fossils. Those that survived are the success stories. Natural materials are mostly formed from organics, inorganic crystals and amorphous phases. The materials make economic sense by optimizing the design of the structures or systems to meet multiple needs. We constantly "see" many similar strategies in approaches, between man and nature, but we seldom look at the details of natures approaches. The power of image processing, in many of natures creatures, is a detail that is often overlooked. Seldon does the engineer interact with the biologist and learn what nature has to teach us. The variety and complexity of biological materials and the optical systems formed should inspire us.

  6. Tomographic imaging system

    International Nuclear Information System (INIS)

    Hayakawa, T.; Horiba, I.; Kohno, H.; Nakaya, C.; Sekihara, K.; Shiono, H.; Tomura, T.; Yamamoto, S.; Yanaka, S.

    1980-01-01

    A tomographic imaging system comprising: irradiating means for irradating a cross-section of an object under consideration with radiation rays from plural directions; detector means for detecting the radiation rays transmitted through the cross-section of said object to produce an output signal; first memory means for storing the output signal of said detector means; and an image jreconstructing section for performing a convolution integral operation on the contents of said first memory means by means of a first weighting function to reconstruct a three-dimensional image of the cross-section of said object, said image reconstructing section including (I) second memory means for storing a second weighting function, said second weighting function being provided with a predetermined positive and negative (N-1)th order when the output signal of said detector means produced by the irradiation of the cross-section of said object from one of said plural directions is sampled by N points, the value of the (N-1)th order of said second weighting function being an integration of said first weighting function from the (N-1)th order to positive infinity and the value of -(N-1)th order of said second weighting function being an integration of said first weighting function from the -(N-1)th order to negative infinity, (II) control means for successively reading out the contents of said first and second memory means, and (III) operational means for performing multiplying and summing operations on the read-out contents of said first and second memory means, said operational means producing the product of the values fo the (N-1)th and -(N-1)th orders of said second weighting function and a component of the output signal of said detector means relating to the radiation rays free from the absorption thereof by said object

  7. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  8. Quantitative imaging of single upconversion nanoparticles in biological tissue.

    Directory of Open Access Journals (Sweden)

    Annemarie Nadort

    Full Text Available The unique luminescent properties of new-generation synthetic nanomaterials, upconversion nanoparticles (UCNPs, enabled high-contrast optical biomedical imaging by suppressing the crowded background of biological tissue autofluorescence and evading high tissue absorption. This raised high expectations on the UCNP utilities for intracellular and deep tissue imaging, such as whole animal imaging. At the same time, the critical nonlinear dependence of the UCNP luminescence on the excitation intensity results in dramatic signal reduction at (∼1 cm depth in biological tissue. Here, we report on the experimental and theoretical investigation of this trade-off aiming at the identification of optimal application niches of UCNPs e.g. biological liquids and subsurface tissue layers. As an example of such applications, we report on single UCNP imaging through a layer of hemolyzed blood. To extend this result towards in vivo applications, we quantified the optical properties of single UCNPs and theoretically analyzed the prospects of single-particle detectability in live scattering and absorbing bio-tissue using a human skin model. The model predicts that a single 70-nm UCNP would be detectable at skin depths up to 400 µm, unlike a hardly detectable single fluorescent (fluorescein dye molecule. UCNP-assisted imaging in the ballistic regime thus allows for excellent applications niches, where high sensitivity is the key requirement.

  9. High sensitivity optical molecular imaging system

    Science.gov (United States)

    An, Yu; Yuan, Gao; Huang, Chao; Jiang, Shixin; Zhang, Peng; Wang, Kun; Tian, Jie

    2018-02-01

    Optical Molecular Imaging (OMI) has the advantages of high sensitivity, low cost and ease of use. By labeling the regions of interest with fluorescent or bioluminescence probes, OMI can noninvasively obtain the distribution of the probes in vivo, which play the key role in cancer research, pharmacokinetics and other biological studies. In preclinical and clinical application, the image depth, resolution and sensitivity are the key factors for researchers to use OMI. In this paper, we report a high sensitivity optical molecular imaging system developed by our group, which can improve the imaging depth in phantom to nearly 5cm, high resolution at 2cm depth, and high image sensitivity. To validate the performance of the system, special designed phantom experiments and weak light detection experiment were implemented. The results shows that cooperated with high performance electron-multiplying charge coupled device (EMCCD) camera, precision design of light path system and high efficient image techniques, our OMI system can simultaneously collect the light-emitted signals generated by fluorescence molecular imaging, bioluminescence imaging, Cherenkov luminance and other optical imaging modality, and observe the internal distribution of light-emitting agents fast and accurately.

  10. Omics/systems biology and cancer cachexia.

    Science.gov (United States)

    Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

    2016-06-01

    Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

  11. Decision Making in Biological Systems

    DEFF Research Database (Denmark)

    Tian, Chengzhe

    This thesis consists of five projects in three topics with a shared theme of understanding cellular decision-making processes with mathematical modeling. In the first topic, we address the possible interaction between bacterial Toxin-Antitoxin (TA) systems and stringent response alarmone guanosin...

  12. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  13. Acoustic imaging system

    Science.gov (United States)

    Smith, Richard W.

    1979-01-01

    An acoustic imaging system for displaying an object viewed by a moving array of transducers as the array is pivoted about a fixed point within a given plane. A plurality of transducers are fixedly positioned and equally spaced within a laterally extending array and operatively directed to transmit and receive acoustic signals along substantially parallel transmission paths. The transducers are sequentially activated along the array to transmit and receive acoustic signals according to a preestablished sequence. Means are provided for generating output voltages for each reception of an acoustic signal, corresponding to the coordinate position of the object viewed as the array is pivoted. Receptions from each of the transducers are presented on the same display at coordinates corresponding to the actual position of the object viewed to form a plane view of the object scanned.

  14. Nuclear medicine imaging system

    Science.gov (United States)

    Bennett, Gerald W.; Brill, A. Bertrand; Bizais, Yves J. C.; Rowe, R. Wanda; Zubal, I. George

    1986-01-01

    A nuclear medicine imaging system having two large field of view scintillation cameras mounted on a rotatable gantry and being movable diametrically toward or away from each other is disclosed. In addition, each camera may be rotated about an axis perpendicular to the diameter of the gantry. The movement of the cameras allows the system to be used for a variety of studies, including positron annihilation, and conventional single photon emission, as well as static orthogonal dual multi-pinhole tomography. In orthogonal dual multi-pinhole tomography, each camera is fitted with a seven pinhole collimator to provide seven views from slightly different perspectives. By using two cameras at an angle to each other, improved sensitivity and depth resolution is achieved. The computer system and interface acquires and stores a broad range of information in list mode, including patient physiological data, energy data over the full range detected by the cameras, and the camera position. The list mode acquisition permits the study of attenuation as a result of Compton scatter, as well as studies involving the isolation and correlation of energy with a range of physiological conditions.

  15. Biological imaging by soft X-ray diffraction microscopy

    Science.gov (United States)

    Shapiro, David

    We have developed a microscope for soft x-ray diffraction imaging of dry or frozen hydrated biological specimens. This lensless imaging system does not suffer from the resolution or specimen thickness limitations that other short wavelength microscopes experience. The microscope, currently situated at beamline 9.0.1 of the Advanced Light Source, can collect diffraction data to 12 nm resolution with 750 eV photons and 17 nm resolution with 520 eV photons. The specimen can be rotated with a precision goniometer through an angle of 160 degrees allowing for the collection of nearly complete three-dimensional diffraction data. The microscope is fully computer controlled through a graphical user interface and a scripting language automates the collection of both two-dimensional and three-dimensional data. Diffraction data from a freeze-dried dwarf yeast cell, Saccharomyces cerevisiae carrying the CLN3-1 mutation, was collected to 12 run resolution from 8 specimen orientations spanning a total rotation of 8 degrees. The diffraction data was phased using the difference map algorithm and the reconstructions provide real space images of the cell to 30 nm resolution from each of the orientations. The agreement of the different reconstructions provides confidence in the recovered, and previously unknown, structure and indicates the three dimensionality of the cell. This work represents the first imaging of the natural complex refractive contrast from a whole unstained cell by the diffraction microscopy method and has achieved a resolution superior to lens based x-ray tomographic reconstructions of similar specimens. Studies of the effects of exposure to large radiation doses were also carried out. It was determined that the freeze-dried cell suffers from an initial collapse, which is followed by a uniform, but slow, shrinkage. This structural damage to the cell is not accompanied by a diminished ability to see small features in the specimen. Preliminary measurements on frozen

  16. Systems Biology and Stem Cell Pluripotency

    DEFF Research Database (Denmark)

    Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

    2016-01-01

    Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

  17. Tunable promoters in synthetic and systems biology

    DEFF Research Database (Denmark)

    Dehli, Tore; Solem, Christian; Jensen, Peter Ruhdal

    2012-01-01

    in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available......Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central...... for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression...

  18. Experimental image alignment system

    Science.gov (United States)

    Moyer, A. L.; Kowel, S. T.; Kornreich, P. G.

    1980-01-01

    A microcomputer-based instrument for image alignment with respect to a reference image is described which uses the DEFT sensor (Direct Electronic Fourier Transform) for image sensing and preprocessing. The instrument alignment algorithm which uses the two-dimensional Fourier transform as input is also described. It generates signals used to steer the stage carrying the test image into the correct orientation. This algorithm has computational advantages over algorithms which use image intensity data as input and is suitable for a microcomputer-based instrument since the two-dimensional Fourier transform is provided by the DEFT sensor.

  19. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

    Science.gov (United States)

    De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

    2010-03-01

    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

  20. 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.

  1. Synchronous ultrasonic Doppler imaging of magnetic microparticles in biological tissues

    Energy Technology Data Exchange (ETDEWEB)

    Pyshnyi, Michael Ph. [Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119991 (Russian Federation); Kuznetsov, Oleg A. [Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119991 (Russian Federation)], E-mail: kuznetsov_oa@yahoo.com; Pyshnaya, Svetlana V.; Nechitailo, Galina S.; Kuznetsov, Anatoly A. [Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119991 (Russian Federation)

    2009-05-15

    We considered applicability of acoustic imaging technology for the detection of magnetic microparticles and nanoparticles inside soft biological tissues. Such particles are widely used for magnetically targeted drug delivery and magnetic hyperthermia. We developed a new method of ultrasonic synchronous tissue Doppler imaging with magnetic modulation for in vitro and in vivo detection and visualization of magnetic ultradisperse objects in soft tissues. Prototype hardware with appropriate software was produced and the method was successfully tested on magnetic microparticles injected into an excised pig liver.

  2. Synchronous ultrasonic Doppler imaging of magnetic microparticles in biological tissues

    International Nuclear Information System (INIS)

    Pyshnyi, Michael Ph.; Kuznetsov, Oleg A.; Pyshnaya, Svetlana V.; Nechitailo, Galina S.; Kuznetsov, Anatoly A.

    2009-01-01

    We considered applicability of acoustic imaging technology for the detection of magnetic microparticles and nanoparticles inside soft biological tissues. Such particles are widely used for magnetically targeted drug delivery and magnetic hyperthermia. We developed a new method of ultrasonic synchronous tissue Doppler imaging with magnetic modulation for in vitro and in vivo detection and visualization of magnetic ultradisperse objects in soft tissues. Prototype hardware with appropriate software was produced and the method was successfully tested on magnetic microparticles injected into an excised pig liver.

  3. Systems biology solutions for biochemical production challenges

    DEFF Research Database (Denmark)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

    2017-01-01

    There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...... characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

  4. Systems biology solutions for biochemical production challenges.

    Science.gov (United States)

    Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

    2017-06-01

    There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Wavelet analysis of biological tissue's Mueller-matrix images

    Science.gov (United States)

    Tomka, Yu. Ya.

    2008-05-01

    The interrelations between statistics of the 1st-4th orders of the ensemble of Mueller-matrix images and geometric structure of birefringent architectonic nets of different morphological structure have been analyzed. The sensitivity of asymmetry and excess of statistic distributions of matrix elements Cik to changing of orientation structure of optically anisotropic protein fibrils of physiologically normal and pathologically changed biological tissues architectonics has been shown.

  6. 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

    2014-07-07

    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.

  7. An Ibm PC/AT-Based Image Acquisition And Processing System For Quantitative Image Analysis

    Science.gov (United States)

    Kim, Yongmin; Alexander, Thomas

    1986-06-01

    In recent years, a large number of applications have been developed for image processing systems in the area of biological imaging. We have already finished the development of a dedicated microcomputer-based image processing and analysis system for quantitative microscopy. The system's primary function has been to facilitate and ultimately automate quantitative image analysis tasks such as the measurement of cellular DNA contents. We have recognized from this development experience, and interaction with system users, biologists and technicians, that the increasingly widespread use of image processing systems, and the development and application of new techniques for utilizing the capabilities of such systems, would generate a need for some kind of inexpensive general purpose image acquisition and processing system specially tailored for the needs of the medical community. We are currently engaged in the development and testing of hardware and software for a fairly high-performance image processing computer system based on a popular personal computer. In this paper, we describe the design and development of this system. Biological image processing computer systems have now reached a level of hardware and software refinement where they could become convenient image analysis tools for biologists. The development of a general purpose image processing system for quantitative image analysis that is inexpensive, flexible, and easy-to-use represents a significant step towards making the microscopic digital image processing techniques more widely applicable not only in a research environment as a biologist's workstation, but also in clinical environments as a diagnostic tool.

  8. Synthetic Biology: Advancing Biological Frontiers by Building Synthetic Systems

    OpenAIRE

    Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D

    2012-01-01

    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

  9. Systems Biology — the Broader Perspective

    Directory of Open Access Journals (Sweden)

    Jonathan Bard

    2013-06-01

    Full Text Available Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form [process] (e.g., [activates] . Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future.

  10. OSPACS: Ultrasound image management system

    Directory of Open Access Journals (Sweden)

    Bessant Conrad

    2008-06-01

    Full Text Available Abstract Background Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and communication system (PACS for storing and retrieving such images. However, these systems are usually not suitable for managing large collections of anonymized ultrasound images gathered during a clinical screening trial. Results We have developed a system enabling the accurate archiving and management of ultrasound images gathered during a clinical screening trial. It is based upon a Windows application utilizing an open-source DICOM image viewer and a relational database. The system automates the bulk import of DICOM files from removable media by cross-validating the patient information against an external database, anonymizing the data as well as the image, and then storing the contents of the file as a field in a database record. These image records may then be retrieved from the database and presented in a tree-view control so that the user can select particular images for display in a DICOM viewer or export them to external media. Conclusion This system provides error-free automation of ultrasound image archiving and management, suitable for use in a clinical trial. An open-source project has been established to promote continued development of the system.

  11. 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.

  12. Central nervous system imaging

    International Nuclear Information System (INIS)

    Anon.

    1987-01-01

    Since its introduction in 1973, computed tomography (CT) of the brain has had a revolutionary impact on neuroradiologic diagnosis. It has largely replaced radionuclide brain imaging as the initial, noninvasive neurologic screening examination. Although conventional radionuclide brain imaging still contributes useful and unique diagnostic information in a few clinical situations, it appears that new technology and applications must be found if nuclear imaging is to play a prominent future role in neurologic diagnosis as it did in the past. One of the main advantages of CT over radionuclide brain imaging at present is CT's ability to demonstrate the size, shape, and position of the cerebral ventricles and subarachnoid spaces. Another important strength of CT is the ability to differentiate ischemic cerebral infarction from intracerebral hemorrhage. The overall sensitivity of CT in detecting intracranial neoplasms is also greater than that of radionuclide brain imaging, and CT is very useful in demonstrating the effects of head trauma. Magnetic resonance imaging appears superior to CT in the evaluation of neurologic disorders. A renewed interest in radionuclide brain imaging has developed because of recent advances in emission computed tomographic imaging. When tracer kinetic models are used, cerebral blood flow (CBF), blood volume, metabolic rate, and glucose and amino acid transport can be measured. Other applications involve investigation of receptor bindings, evaluation of the blood-brain barrier, brain blood-volume measurement, and cisternography

  13. Systems Biology for Organotypic Cell Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Grego, Sonia [RTI International, Research Triangle Park, NC (United States); Dougherty, Edward R. [Texas A & M Univ., College Station, TX (United States); Alexander, Francis J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Auerbach, Scott S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Berridge, Brian R. [GlaxoSmithKline, Research Triangle Park, NC (United States); Bittner, Michael L. [Translational Genomics Research Inst., Phoenix, AZ (United States); Casey, Warren [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Cooley, Philip C. [RTI International, Research Triangle Park, NC (United States); Dash, Ajit [HemoShear Therapeutics, Charlottesville, VA (United States); Ferguson, Stephen S. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Fennell, Timothy R. [RTI International, Research Triangle Park, NC (United States); Hawkins, Brian T. [RTI International, Research Triangle Park, NC (United States); Hickey, Anthony J. [RTI International, Research Triangle Park, NC (United States); Kleensang, Andre [Johns Hopkins Univ., Baltimore, MD (United States). Center for Alternatives to Animal Testing; Liebman, Michael N. [IPQ Analytics, Kennett Square, PA (United States); Martin, Florian [Phillip Morris International, Neuchatel (Switzerland); Maull, Elizabeth A. [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Paragas, Jason [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Qiao, Guilin [Defense Threat Reduction Agency, Ft. Belvoir, VA (United States); Ramaiahgari, Sreenivasa [National Inst. of Environmental Health Sciences, Research Triangle Park, NC (United States); Sumner, Susan J. [RTI International, Research Triangle Park, NC (United States); Yoon, Miyoung [The Hamner Inst. for Health Sciences, Research Triangle Park, NC (United States); ScitoVation, Research Triangle Park, NC (United States)

    2016-08-04

    Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, “organotypic” cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of tissue-level physiological responses by integrating empirical data derived from organotypic culture systems with computational models of intracellular pathways to better predict human responses. Successful implementation of this integrated approach will provide a powerful tool for faster, more accurate and cost-effective screening of potential toxicants and therapeutics. On September 11, 2015, an interdisciplinary group of scientists, engineers, and clinicians gathered for a workshop in Research Triangle Park, North Carolina, to discuss this ambitious goal. Participants represented laboratory-based and computational modeling approaches to pharmacology and toxicology, as well as the pharmaceutical industry, government, non-profits, and academia. Discussions focused on identifying critical system perturbations to model, the computational tools required, and the experimental approaches best suited to generating key data. This consensus report summarizes the discussions held.

  14. Spatially modulated imaging system

    International Nuclear Information System (INIS)

    Barrett, H.H.

    1975-01-01

    Noncoherent radiation, such as x-rays, is spatially coded, directed through an object and spatially detected to form a spatially coded pattern, from which an image of the object may be reconstructed. The x-ray source may be formed by x-ray fluorescence and substration of the holographic images formed by two sources having energy levels predominantly above and below the maximum absorption range of an agent in the object may be used to enhance contrast in the reproduced image. (Patent Office Record)

  15. Photoacoustic imaging in both soft and hard biological tissue

    International Nuclear Information System (INIS)

    Li, T; Dewhurst, R J

    2010-01-01

    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.

  16. 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.

  17. Promoting Systems Thinking through Biology Lessons

    Science.gov (United States)

    Riess, Werner; Mischo, Christoph

    2010-01-01

    This study's goal was to analyze various teaching approaches within the context of natural science lessons, especially in biology. The main focus of the paper lies on the effectiveness of different teaching methods in promoting systems thinking in the field of Education for Sustainable Development. The following methods were incorporated into the…

  18. Systems Biology of Glucocorticoids in Muscle Disease

    Science.gov (United States)

    2010-10-01

    Introduction Duchenne muscular dystrophy (DMD) is the most common and incurable muscular dystrophy of childhood. Muscle regeneration fails with...SUBJECT TERMS Duchenne Muscular dystrophy , Glucocorticoids, Systems biology, Drug mechanism 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION...better targeted and more effective therapies for Duchenne muscular dystrophy dynamically. This MDA grant proposal is led by Dr. Eric Hoffman, and it

  19. Modular microfluidic system for biological sample preparation

    Science.gov (United States)

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  20. Radiological/biological/aerosol removal system

    Science.gov (United States)

    Haslam, Jeffery J

    2015-03-17

    An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

  1. Notions of radiation chemistry in biological systems

    International Nuclear Information System (INIS)

    Mastro, N.L. del.

    1989-10-01

    The present paper examines some aspects of the direct and indirect biological radiation effects: pair formation, free radicals, superoxide ion, hydrogen peroxide, hydroxyl radical, oxygen singlet together with the endogen radioprotector mechanisms of organisms and the ways in which an improved radioresistance of biochemical systems can be achieved. (author) [pt

  2. New image-stabilizing system

    Science.gov (United States)

    Zhao, Yuejin

    1996-06-01

    In this paper, a new method for image stabilization with a three-axis image- stabilizing reflecting prism assembly is presented, and the principle of image stabilization in this prism assembly, formulae for image stabilization and working formulae with an approximation up to the third power are given in detail. In this image-stabilizing system, a single chip microcomputer is used to calculate value of compensating angles and thus to control the prism assembly. Two gyroscopes act as sensors from which information of angular perturbation is obtained, three stepping motors drive the prism assembly to compensate for the movement of image produced by angular perturbation. The image-stabilizing device so established is a multifold system which involves optics, mechanics, electronics and computer.

  3. Integrative Systems Biology Applied to Toxicology

    DEFF Research Database (Denmark)

    Kongsbak, Kristine Grønning

    associated with combined exposure to multiple chemicals. Testing all possible combinations of the tens of thousands environmental chemicals is impractical. This PhD project was launched to apply existing computational systems biology methods to toxicological research. In this thesis, I present in three...... of a system thereby suggesting new ways of thinking specific toxicological endpoints. Furthermore, computational methods can serve as valuable input for the hypothesis generating phase of the preparations of a research project....

  4. PET imaging of the autonomic nervous system

    International Nuclear Information System (INIS)

    THACKERAY, James T.; BENGEL, Frank M.

    2016-01-01

    The autonomic nervous system is the primary extrinsic control of heart rate and contractility, and is subject to adaptive and maladaptive changes in cardiovascular disease. Consequently, noninvasive assessment of neuronal activity and function is an attractive target for molecular imaging. A myriad of targeted radiotracers have been developed over the last 25 years for imaging various components of the sympathetic and parasympathetic signal cascades. While routine clinical use remains somewhat limited, a number of larger scale studies in recent years have supplied momentum to molecular imaging of autonomic signaling. Specifically, the findings of the ADMIRE HF trial directly led to United States Food and Drug Administration approval of 123I-metaiodobenzylguanidine (MIBG) for Single Photon Emission Computed Tomography (SPECT) assessment of sympathetic neuronal innervation, and comparable results have been reported using the analogous PET agent 11C-meta-hydroxyephedrine (HED). Due to the inherent capacity for dynamic quantification and higher spatial resolution, regional analysis may be better served by PET. In addition, preliminary clinical and extensive preclinical experience has provided a broad foundation of cardiovascular applications for PET imaging of the autonomic nervous system. Recent years have witnessed the growth of novel quantification techniques, expansion of multiple tracer studies, and improved understanding of the uptake of different radiotracers, such that the transitional biology of dysfunctional subcellular catecholamine handling can be distinguished from complete denervation. As a result, sympathetic neuronal molecular imaging is poised to play a role in individualized patient care, by stratifying cardiovascular risk, visualizing underlying biology, and guiding and monitoring therapy.

  5. Advances in Small Animal Imaging Systems

    International Nuclear Information System (INIS)

    Loudos, George K.

    2007-01-01

    The rapid growth in genetics and molecular biology combined with the development of techniques for genetically engineering small animals has led to an increased interest in in vivo laboratory animal imaging during the past few years. For this purpose, new instrumentation, data acquisition strategies, and image processing and reconstruction techniques are being developed, researched and evaluated. The aim of this article is to give a short overview of the state of the art technologies for high resolution and high sensitivity molecular imaging techniques, primarily positron emission tomography (PET) and single photon emission computed tomography (SPECT). The basic needs of small animal imaging will be described. The evolution in instrumentation in the past two decades, as well as the commercially available systems will be overviewed. Finally, the new trends in detector technology and preliminary results from challenging applications will be presented. For more details a number of references are provided

  6. Biologically inspired EM image alignment and neural reconstruction.

    Science.gov (United States)

    Knowles-Barley, Seymour; Butcher, Nancy J; Meinertzhagen, Ian A; Armstrong, J Douglas

    2011-08-15

    Three-dimensional reconstruction of consecutive serial-section transmission electron microscopy (ssTEM) images of neural tissue currently requires many hours of manual tracing and annotation. Several computational techniques have already been applied to ssTEM images to facilitate 3D reconstruction and ease this burden. Here, we present an alternative computational approach for ssTEM image analysis. We have used biologically inspired receptive fields as a basis for a ridge detection algorithm to identify cell membranes, synaptic contacts and mitochondria. Detected line segments are used to improve alignment between consecutive images and we have joined small segments of membrane into cell surfaces using a dynamic programming algorithm similar to the Needleman-Wunsch and Smith-Waterman DNA sequence alignment procedures. A shortest path-based approach has been used to close edges and achieve image segmentation. Partial reconstructions were automatically generated and used as a basis for semi-automatic reconstruction of neural tissue. The accuracy of partial reconstructions was evaluated and 96% of membrane could be identified at the cost of 13% false positive detections. An open-source reference implementation is available in the Supplementary information. seymour.kb@ed.ac.uk; douglas.armstrong@ed.ac.uk Supplementary data are available at Bioinformatics online.

  7. Army medical imaging system: ARMIS

    International Nuclear Information System (INIS)

    Siedband, M.P.; Kramp, D.C.

    1987-01-01

    Recent advances of stimulable phosphor screens, data cards using optical storage means, and new personal computers with image processing capability have made possible the design of economical filmless medical imaging systems. The addition of communication links means that remote interpretation of images is also possible. The Army Medical Imaging System uses stimulable phosphor screens, digital readout, a small computer, an optical digital data card device, and a DIN/PACS link. Up to 200 images can be stored in the computer hard disk for rapid recall and reading by the radiologist. The computer permits image processing, annotation, insertion of text, and control of the system. Each device contains an image storage RAM and communicates with the computer via the small computer systems interface. Data compression is used to reduce the required storage capacity and transmission times of the 1-mB images. The credit card-size optical data cards replace film and can store 12 or more images. The data cards can be read on an independent viewer. The research is supported by the U.S. Army Biomedical Research and Development Laboratory

  8. Optical Time-of-Flight and Absorbance Imaging of Biologic Media

    Science.gov (United States)

    Benaron, David A.; Stevenson, David K.

    1993-03-01

    Imaging the interior of living bodies with light may assist in the diagnosis and treatment of a number of clinical problems, which include the early detection of tumors and hypoxic cerebral injury. An existing picosecond time-of-flight and absorbance (TOFA) optical system has been used to image a model biologic system and a rat. Model measurements confirmed TOFA principles in systems with a high degree of photon scattering; rat images, which were constructed from the variable time delays experienced by a fixed fraction of early-arriving transmitted photons, revealed identifiable internal structure. A combination of light-based quantitative measurement and TOFA localization may have applications in continuous, noninvasive monitoring for structural imaging and spatial chemometric analysis in humans.

  9. Automated setpoint adjustment for biological contact mode atomic force microscopy imaging

    International Nuclear Information System (INIS)

    Casuso, Ignacio; Scheuring, Simon

    2010-01-01

    Contact mode atomic force microscopy (AFM) is the most frequently used AFM imaging mode in biology. It is about 5-10 times faster than oscillating mode imaging (in conventional AFM setups), and provides topographs of biological samples with sub-molecular resolution and at a high signal-to-noise ratio. Unfortunately, contact mode imaging is sensitive to the applied force and intrinsic force drift: inappropriate force applied by the AFM tip damages the soft biological samples. We present a methodology that automatically searches for and maintains high resolution imaging forces. We found that the vertical and lateral vibrations of the probe during scanning are valuable signals for the characterization of the actual applied force by the tip. This allows automated adjustment and correction of the setpoint force during an experiment. A system that permanently performs this methodology steered the AFM towards high resolution imaging forces and imaged purple membrane at molecular resolution and live cells at high signal-to-noise ratio for hours without an operator.

  10. Underwater laser imaging system (UWLIS)

    Energy Technology Data Exchange (ETDEWEB)

    DeLong, M. [Lawrence Livermore National Lab., CA (United States)

    1994-11-15

    Practical limitations with underwater imaging systems area reached when the noise in the back scattered radiation generated in the water between the imaging system and the target obscures the spatial contrast and resolution necessary for target discovery and identification. The advent of high power lasers operating in the blue-green portion of the visible spectrum (oceanic transmission window) has led to improved experimental illumination systems for underwater imaging. Range-gated and synchronously scanned devices take advantage of the unique temporal and spatial coherence properties of laser radiation, respectively, to overcome the deleterious effects of common volume back scatter.

  11. 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.

  12. Set membership experimental design for biological systems

    Directory of Open Access Journals (Sweden)

    Marvel Skylar W

    2012-03-01

    Full Text Available Abstract Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This

  13. Semiautomatic digital imaging system for cytogenetic analysis

    International Nuclear Information System (INIS)

    Chaubey, R.C.; Chauhan, P.C.; Bannur, S.V.; Kulgod, S.V.; Chadda, V.K.; Nigam, R.K.

    1999-08-01

    The paper describes a digital image processing system, developed indigenously at BARC for size measurement of microscopic biological objects such as cell, nucleus and micronucleus in mouse bone marrow; cytochalasin-B blocked human lymphocytes in-vitro; numerical counting and karyotyping of metaphase chromosomes of human lymphocytes. Errors in karyotyping of chromosomes by the imaging system may creep in due to lack of well-defined position of centromere or extensive bending of chromosomes, which may result due to poor quality of preparation. Good metaphase preparations are mandatory for precise and accurate analysis by the system. Additional new morphological parameters about each chromosome have to be incorporated to improve the accuracy of karyotyping. Though the experienced cytogenetisist is the final judge; however, the system assists him/her to carryout analysis much faster as compared to manual scoring. Further, experimental studies are in progress to validate different software packages developed for various cytogenetic applications. (author)

  14. Optoelectronic system and apparatus for connection to biological systems

    Science.gov (United States)

    Okandan, Murat; Nielson, Gregory N.

    2018-03-06

    The present invention relates to a biological probe structure, as well as apparatuses, systems, and methods employing this structure. In particular embodiments, the structure includes a hermetically sealed unit configured to receive and transmit one or more optical signals. Furthermore, the structure can be implanted subcutaneously and interrogated externally. In this manner, a minimally invasive method can be employed to detect, treat, and/or assess the biological target. Additional methods and systems are also provided.

  15. A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

    Science.gov (United States)

    Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

    2016-06-17

    Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

  16. 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. ...

  17. Combining different modalities for 3D imaging of biological objects

    International Nuclear Information System (INIS)

    Tsyganov, Eh.; Antich, P.; Kulkarni, P.; Mason, R.; Parkey, R.; Seliuonine, S.; Shay, J.; Soesbe, T.; Zhezher, V.; Zinchenko, A.

    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, 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. This structural information can provide even more detail if the x-ray tomography is used as presented in the paper

  18. Stereoscopic medical imaging collaboration system

    Science.gov (United States)

    Okuyama, Fumio; Hirano, Takenori; Nakabayasi, Yuusuke; Minoura, Hirohito; Tsuruoka, Shinji

    2007-02-01

    The computerization of the clinical record and the realization of the multimedia have brought improvement of the medical service in medical facilities. It is very important for the patients to obtain comprehensible informed consent. Therefore, the doctor should plainly explain the purpose and the content of the diagnoses and treatments for the patient. We propose and design a Telemedicine Imaging Collaboration System which presents a three dimensional medical image as X-ray CT, MRI with stereoscopic image by using virtual common information space and operating the image from a remote location. This system is composed of two personal computers, two 15 inches stereoscopic parallax barrier type LCD display (LL-151D, Sharp), one 1Gbps router and 1000base LAN cables. The software is composed of a DICOM format data transfer program, an operation program of the images, the communication program between two personal computers and a real time rendering program. Two identical images of 512×768 pixcels are displayed on two stereoscopic LCD display, and both images show an expansion, reduction by mouse operation. This system can offer a comprehensible three-dimensional image of the diseased part. Therefore, the doctor and the patient can easily understand it, depending on their needs.

  19. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

  20. Complex biological and bio-inspired systems

    Energy Technology Data Exchange (ETDEWEB)

    Ecke, Robert E [Los Alamos National Laboratory

    2009-01-01

    The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

  1. AFM imaging of functionalized carbon nanotubes on biological membranes

    International Nuclear Information System (INIS)

    Lamprecht, C; Danzberger, J; Rangl, M; Gruber, H J; Hinterdorfer, P; Kienberger, F; Ebner, A; Liashkovich, I; Neves, V; Heister, E; Coley, H M; McFadden, J; Flahaut, E

    2009-01-01

    Multifunctional carbon nanotubes are promising for biomedical applications as their nano-size, together with their physical stability, gives access into the cell and various cellular compartments including the nucleus. However, the direct and label-free detection of carbon nanotube uptake into cells is a challenging task. The atomic force microscope (AFM) is capable of resolving details of cellular surfaces at the nanometer scale and thus allows following of the docking of carbon nanotubes to biological membranes. Here we present topographical AFM images of non-covalently functionalized single walled (SWNT) and double walled carbon nanotubes (DWNT) immobilized on different biological membranes, such as plasma membranes and nuclear envelopes, as well as on a monolayer of avidin molecules. We were able to visualize DWNT on the nuclear membrane while at the same time resolving individual nuclear pore complexes. Furthermore, we succeeded in localizing individual SWNT at the border of incubated cells and in identifying bundles of DWNT on cell surfaces by AFM imaging.

  2. Assessment of biological leaf tissue using biospeckle laser imaging technique

    Science.gov (United States)

    Ansari, M. Z.; Mujeeb, A.; Nirala, A. K.

    2018-06-01

    We report on the application of an optical imaging technique, the biospeckle laser, as a potential tool to assess biological and medicinal plant leaves. The biospeckle laser technique is a non-invasive and non-destructive optical technique used to investigate biological objects. Just after their removal from plants, the torn leaves were used for biospeckle laser imaging. Quantitative evaluation of the biospeckle data using the inertia moment (IM) of the time history speckle pattern, showed that the IM can be utilized to provide a biospeckle signature to the plant leaves. It showed that leaves from different plants can have their own characteristic IM values. We further investigated the infected regions of the leaves that display a relatively lower biospeckle activity than the healthy tissue. It was easy to discriminate between the infected and healthy regions of the leaf tissue. The biospeckle technique can successfully be implemented as a potential tool for the taxonomy of quality leaves. Furthermore, the technique can help boost the quality of ayurvedic medicines.

  3. Life: An Introduction to Complex Systems Biology

    CERN Document Server

    Kaneko, Kunihiko

    2006-01-01

    What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there? This book examines life not from the reductionist point of view, but rather asks the question: what are the universal properties of living systems and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.

  4. 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.

  5. System biology and the project Encode

    Directory of Open Access Journals (Sweden)

    M. Yu. Obolenskaya

    2014-08-01

    Full Text Available The goal of this review is to give an incipient knowledge on the background of system biology, the premises to its assignment as a new branch of biology, its principles, methodology and its great achievements in identification of functional elements of human genome and regulation of their concordant­ and differential activity. The short characteristics of functional elements including the protein-coding sequences and those coding noncoding RNAs, the DNAse 1 hypersensitivity sites and methylated CpG islets, modified histones and specific 3D structure of chromatin, are represented. The topology of transcription factors network with its main motifs, hierar­chy, combination and association of transcription factors and their allelic specificity are highlighted­.

  6. Engineering biological systems toward a sustainable bioeconomy.

    Science.gov (United States)

    Lopes, Mateus Schreiner Garcez

    2015-06-01

    The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy.

  7. Biological Therapy in Systemic Lupus Erythematosus

    Directory of Open Access Journals (Sweden)

    Mariana Postal

    2012-01-01

    Full Text Available Systemic lupus erythematosus (SLE is a prototypic inflammatory autoimmune disorder characterized by multisystem involvement and fluctuating disease activity. Symptoms range from rather mild manifestations such as rash or arthritis to life-threatening end-organ manifestations. Despite new and improved therapy having positively impacted the prognosis of SLE, a subgroup of patients do not respond to conventional therapy. Moreover, the risk of fatal outcomes and the damaging side effects of immunosuppressive therapies in SLE call for an improvement in the current therapeutic management. New therapeutic approaches are focused on B-cell targets, T-cell downregulation and costimulatory blockade, cytokine inhibition, and the modulation of complement. Several biological agents have been developed, but this encouraging news is associated with several disappointments in trials and provide a timely moment to reflect on biologic therapy in SLE.

  8. Artificial intelligence and medical imaging. Expert systems and image analysis

    International Nuclear Information System (INIS)

    Wackenheim, A.; Zoellner, G.; Horviller, S.; Jacqmain, T.

    1987-01-01

    This paper gives an overview on the existing systems for automated image analysis and interpretation in medical imaging, especially in radiology. The example of ORFEVRE, the system for the analysis of CAT-scan images of the cervical triplet (c3-c5) by image analysis and subsequent expert-system is given and discussed in detail. Possible extensions are described [fr

  9. A Diagnostic Ultrasound Imaging System

    International Nuclear Information System (INIS)

    Lee, Seong Woo

    1999-01-01

    The ability to see the internal organs of the human body in a noninvasive way is a powerful diagnostic tool of modern medicine. Among these imaging modalities such as X-ray, MRI, and ultrasound. MRI and ultrasound are presenting much less risk of undesirable damage of both patient and examiner. In fact, no deleterious effects have been reported as a result of clinical examination by using MRI and ultrasound diagnostic equipment. As a result, their market volume has been rapidly increased. MRI has a good resolution. but there are a few disadvantages such as high price. non-real-time imaging capability. and expensive diagnostic cost. On the other hand, the ultrasound imaging system has inherently poor resolution as compared with X-ray and MRI. In spite of its poor resolution, the ultrasound diagnostic equipment is lower in price and has an ability of real-time imaging as compared with the others. As a result, the ultrasound imaging system has become general and essential modality for imaging the internal organs of human body. In this review various researches and developments to enhance the resolution of the ultrasound images are explained and future trends of the ultrasound imaging technology are described

  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. Quantitative phase imaging and differential interference contrast imaging for biological TEM

    International Nuclear Information System (INIS)

    Allman, B.E.; McMahon, P.J.; Barone-Nugent, E.D.; Nugent, E.D.

    2002-01-01

    Full text: Phase microscopy is a central technique in science. An experienced microscopist uses this effect to visualise (edge) structure within transparent samples by slightly defocusing the microscope. Although widespread in optical microscopy, phase contrast transmission electron microscopy (TEM) has not been widely adopted. TEM for biological specimens has largely relied on staining techniques to yield sufficient contrast. We show here a simple method for quantitative TEM phase microscopy that quantifies this phase contrast effect. Starting with conventional, digital, bright field images of the sample, our algorithm provides quantitative phase information independent of the sample's bright field intensity image. We present TEM phase images of a range of stained and unstained, biological and material science specimens. This independent phase and intensity information is then used to emulate a range of phase visualisation images familiar to optical microscopy, e.g. differential interference contrast. The phase images contain features not visible with the other imaging modalities. Further, if the TEM samples have been prepared on a microtome to a uniform thickness, the phase information can be converted into refractive index structure of the specimen. Copyright (2002) Australian Society for Electron Microscopy Inc

  12. 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...

  13. Microprocessor based image processing system

    International Nuclear Information System (INIS)

    Mirza, M.I.; Siddiqui, M.N.; Rangoonwala, A.

    1987-01-01

    Rapid developments in the production of integrated circuits and introduction of sophisticated 8,16 and now 32 bit microprocessor based computers, have set new trends in computer applications. Nowadays the users by investing much less money can make optimal use of smaller systems by getting them custom-tailored according to their requirements. During the past decade there have been great advancements in the field of computer Graphics and consequently, 'Image Processing' has emerged as a separate independent field. Image Processing is being used in a number of disciplines. In the Medical Sciences, it is used to construct pseudo color images from computer aided tomography (CAT) or positron emission tomography (PET) scanners. Art, advertising and publishing people use pseudo colours in pursuit of more effective graphics. Structural engineers use Image Processing to examine weld X-rays to search for imperfections. Photographers use Image Processing for various enhancements which are difficult to achieve in a conventional dark room. (author)

  14. It's the System, Stupid: How Systems Biology Is Transforming.

    Science.gov (United States)

    2010-01-01

    So far, little is known about systems biology and its potential for changing how we diagnose and treat disease. That will change soon, say the systems experts, who advise payers to begin learning now about how it could make healthcare efficient.

  15. Systems Biology: Impressions from a Newcomer Graduate Student in 2016

    Science.gov (United States)

    Simpson, Melanie Rae

    2016-01-01

    As a newcomer, the philosophical basis of systems biology seems intuitive and appealing, the underlying philosophy being that the whole of a living system cannot be completely understood by the study of its individual parts. Yet answers to the questions "What is systems biology?" and "What constitutes a systems biology approach in…

  16. The Feasibility of Systems Thinking in Biology Education

    Science.gov (United States)

    Boersma, Kerst; Waarlo, Arend Jan; Klaassen, Kees

    2011-01-01

    Systems thinking in biology education is an up and coming research topic, as yet with contrasting feasibility claims. In biology education systems thinking can be understood as thinking backward and forward between concrete biological objects and processes and systems models representing systems theoretical characteristics. Some studies claim that…

  17. Biological diversity in the patent system.

    Directory of Open Access Journals (Sweden)

    Paul Oldham

    Full Text Available Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI established by the Global Biodiversity Information Facility (GBIF and Encyclopedia of Life (EOL. We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8-1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on

  18. TissueCypher™: A systems biology approach to anatomic pathology

    Directory of Open Access Journals (Sweden)

    Jeffrey W Prichard

    2015-01-01

    Full Text Available Background: Current histologic methods for diagnosis are limited by intra- and inter-observer variability. Immunohistochemistry (IHC methods are frequently used to assess biomarkers to aid diagnoses, however, IHC staining is variable and nonlinear and the manual interpretation is subjective. Furthermore, the biomarkers assessed clinically are typically biomarkers of epithelial cell processes. Tumors and premalignant tissues are not composed only of epithelial cells but are interacting systems of multiple cell types, including various stromal cell types that are involved in cancer development. The complex network of the tissue system highlights the need for a systems biology approach to anatomic pathology, in which quantification of system processes is combined with informatics tools to produce actionable scores to aid clinical decision-making. Aims: Here, we describe a quantitative, multiplexed biomarker imaging approach termed TissueCypher™ that applies systems biology to anatomic pathology. Applications of TissueCypher™ in understanding the tissue system of Barrett's esophagus (BE and the potential use as an adjunctive tool in the diagnosis of BE are described. Patients and Methods: The TissueCypher™ Image Analysis Platform was used to assess 14 epithelial and stromal biomarkers with known diagnostic significance in BE in a set of BE biopsies with nondysplastic BE with reactive atypia (RA, n = 22 and Barrett's with high-grade dysplasia (HGD, n = 17. Biomarker and morphology features were extracted and evaluated in the confirmed BE HGD cases versus the nondysplastic BE cases with RA. Results: Multiple image analysis features derived from epithelial and stromal biomarkers, including immune biomarkers and morphology, showed significant differences between HGD and RA. Conclusions: The assessment of epithelial cell abnormalities combined with an assessment of cellular changes in the lamina propria may serve as an adjunct to conventional

  19. Nuclear magnetic resonance applications in biological systems

    International Nuclear Information System (INIS)

    Jiang Ling; Liu Maili

    2011-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is a state-of-the-art technology which has been widely applied in biological systems over the past decades. It is a powerful tool for macromolecular structure determination in solution, and has the unique advantage of being capable of elucidating the structure and dynamic behavior of proteins during vital biomedical processes. In this review, we introduce the recent progress in NMR techniques for studying the structure, interaction and dynamics of proteins. The methods for NMR based drug discovery and metabonomics are also briefly introduced. (authors)

  20. System for determining sizes of biological macromolecules

    International Nuclear Information System (INIS)

    Nelson, R.M.; Danby, P.C.

    1987-01-01

    An electrophoresis system for determining the sizes of radiolabelled biological macromolecules is described. It comprises a cell containing an electrophoresis gel and having at least one lane, a voltage source connected across the gel for effecting the movement of macromolecules in the lane, a detector fixed relative to the moving molecules for generating electrical pulses responsive to signals emitted by the radiolabelled molecules; a pulse processor for counting the pulse rate, and a computational device for comparing the pulse rate to a predetermined value. (author)

  1. High-frame-rate imaging of biological samples with optoacoustic micro-tomography

    Science.gov (United States)

    Deán-Ben, X. Luís.; López-Schier, Hernán.; Razansky, Daniel

    2018-02-01

    Optical microscopy remains a major workhorse in biological discovery despite the fact that light scattering limits its applicability to depths of ˜ 1 mm in scattering tissues. Optoacoustic imaging has been shown to overcome this barrier by resolving optical absorption with microscopic resolution in significantly deeper regions. Yet, the time domain is paramount for the observation of biological dynamics in living systems that exhibit fast motion. Commonly, acquisition of microscopy data involves raster scanning across the imaged volume, which significantly limits temporal resolution in 3D. To overcome these limitations, we have devised a fast optoacoustic micro-tomography (OMT) approach based on simultaneous acquisition of 3D image data with a high-density hemispherical ultrasound array having effective detection bandwidth around 25 MHz. We performed experiments by imaging tissue-mimicking phantoms and zebrafish larvae, demonstrating that OMT can provide nearly cellular resolution and imaging speed of 100 volumetric frames per second. As opposed to other optical microscopy techniques, OMT is a hybrid method that resolves optical absorption contrast acoustically using unfocused light excitation. Thus, no penetration barriers are imposed by light scattering in deep tissues, suggesting it as a powerful approach for multi-scale functional and molecular imaging applications.

  2. Images as tools. On visual epistemic practices in the biological sciences.

    Science.gov (United States)

    Samuel, Nina

    2013-06-01

    Contemporary visual epistemic practices in the biological sciences raise new questions of how to transform an iconic data measurements into images, and how the process of an imaging technique may change the material it is 'depicting'. This case-oriented study investigates microscopic imagery, which is used by system and synthetic biologists alike. The core argument is developed around the analysis of two recent methods, developed between 2003 and 2006: localization microscopy and photo-induced cell death. Far from functioning merely as illustrations of work done by other means, images can be determined as tools for discovery in their own right and as objects of investigation. Both methods deploy different constellations of intended and unintended interactions between visual appearance and underlying biological materiality. To characterize these new ways of interaction, the article introduces the notions of 'operational images' and 'operational agency'. Despite all their novelty, operational images are still subject to conventions of seeing and depicting: Phenomena emerging with the new method of localization microscopy have to be designed according to image traditions of older, conventional fluorescence microscopy to function properly as devices for communication between physicists and biologists. The article emerged from a laboratory study based on interviews conducted with researchers from the Kirchhoff-Institute for Physics and German Cancer Research Center (DKFZ) at Bioquant, Heidelberg, in 2011. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. An XCT image database system

    International Nuclear Information System (INIS)

    Komori, Masaru; Minato, Kotaro; Koide, Harutoshi; Hirakawa, Akina; Nakano, Yoshihisa; Itoh, Harumi; Torizuka, Kanji; Yamasaki, Tetsuo; Kuwahara, Michiyoshi.

    1984-01-01

    In this paper, an expansion of X-ray CT (XCT) examination history database to XCT image database is discussed. The XCT examination history database has been constructed and used for daily examination and investigation in our hospital. This database consists of alpha-numeric information (locations, diagnosis and so on) of more than 15,000 cases, and for some of them, we add tree structured image data which has a flexibility for various types of image data. This database system is written by MUMPS database manipulation language. (author)

  4. Distribution and Biological Effects of Nanoparticles in the Reproductive System.

    Science.gov (United States)

    Liu, Ying; Li, Hongxia; Xiao, Kai

    2016-01-01

    Nanoparticles have shown great potential in biomedical applications such as imaging probes and drug delivery. However, the increasing use of nanoparticles has raised concerns about their adverse effects on human health and environment. Reproductive tissues and gametes represent highly delicate biological systems with the essential function of transmitting genetic information to the offspring, which is highly sensitive to environmental toxicants. This review aims to summarzie the penetration of physiological barriers (blood-testis barrier and placental barrier), distribution and biological effects of nanoparticles in the reproductive system, which is essential to control the beneficial effects of nanoparticles applications and to avoid their adverse effects on the reproductive system. We referred to a large number of relevant peer-reviewed research articles about the reproductive toxicity of nanoparticles. The comprehensive information was summarized into two parts: physiological barrier penetration and biological effects of nanoparticles in male or female reproductive system; distribution and metabolism of nanoparticles in the reproductive system. The representative examples were also presented in four tables. The in vitro and in vivo studies imply that some nanoparticles are able to cross the blood-testis barrier or placental barrier, and their penetration depends on the physicochemical characteristics of nanoparticles (e.g., composition, shape, particle size and surface coating). The toxicity assays indicate that nanoparticles might induce adverse physiological effects and impede fertility or embryogenesis. The barrier penetration, adverse physiological effects, distribution and metabolism are closely related to physicochemical characteristics of nanoparticles. Further systematic and mechanistic studies using well-characterized nanoparticles, relevant administration routes, and doses relevant to the expected exposure level are required to improve our

  5. High intensity radiation imaging system

    International Nuclear Information System (INIS)

    Barrett, H.H.

    1976-01-01

    A nuclear imaging system is described for mapping a spatially distributed source of high energy nuclear particles from a living organ which has selectively absorbed a radioactive compound in which the nuclear energy is spatially coded by a zone plate positioned between the source and a spatial detector, and a half tone screen is positioned between the source and the zone plate to increase the definition of the image

  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...... fishes is based on highly laborious chemical analysis. Trichromatic digital imaging and point-wise colorimetric or spectral measurement are also ways of estimating either the redness or the actual astaxanthin concentration of the fillet. These methods all have drawbacks of either cumbersome testing...... are biological parameters with a huge impact on the color and texture of the fish muscle. Consumerdriven quality demands call for rapid methods for quantification of quality parameters such as fat and astaxanthin in the industry. The spectral electromagnetic reflection properties of astaxanthin are well known...

  7. The use contrast agent for imaging biological samples

    Czech Academy of Sciences Publication Activity Database

    Dammer, J.; Weyda, František; Sopko, V.; Jakůbek, J.

    2011-01-01

    Roč. 6, C01096 (2011), s. 1-7 ISSN 1748-0221. [International Workshop on Radiation Imaging Detectors /12./. Cambridge, 11.07.2010-15.7.2010] R&D Projects: GA MŠk 2B06005 Grant - others:Research Program(CZ) 6840770029; Research Program(CZ) 6840770040; GA AV ČR(CZ) IAA600550614; GA MŠk(CZ) 2B06007; GA MŠk(CZ) 1PO4LA211; GA MŠk(CZ) LC06041 Program:IA; 2B; LC Institutional research plan: CEZ:AV0Z50070508 Keywords : x-ray radiography and digital radiography (DR) * x-ray detectors * inspections with x-rays Subject RIV: EA - Cell Biology Impact factor: 1.869, year: 2011

  8. Stepped scanner radiographic imaging system

    International Nuclear Information System (INIS)

    Lapidus, S.N.

    1981-01-01

    The imaging system includes a radiographic camera, a bed for supporting a subject in view of the camera, and a display system. The camera provides X and Y coordinate signals of each radiographic event. The position of the bed relative to the camera is altered sequentially by drive means, between each of a sequence of images provided by the camera. The sequentially occurring images are presented on the display system, each image being positioned on the display in correspondence with the location of the bed relative to the camera. The coordinates of each image point presented on the display is equal to the sum of the respective X and Y coordinate signals from the camera with X and Y coordinate signals provided by a timer which controls the drive means and defines the location of the bed relative to the camera. The camera is electronically decoupled from the display by a gate during movement of the bed relative to the camera from one location to the next location to prevent any smearing effect within the composite image presented on the display. (author)

  9. Dielectric relaxation in biological systems physical principles, methods, and applications

    CERN Document Server

    Feldman, Yuri

    2015-01-01

    This title covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems.

  10. Redefining plant systems biology: from cell to ecosystem

    NARCIS (Netherlands)

    Keurentjes, J.J.B.; Angenent, G.C.; Dicke, M.; Martins Dos Santos, V.A.P.; Molenaar, J.; Van der Putten, W.H.; de Ruiter, P.C.; Struik, P.C.; Thomma, B.P.H.J.

    2011-01-01

    Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase

  11. X-ray diffraction imaging of biological cells

    CERN Document Server

    Nakasako, Masayoshi

    2018-01-01

    In this book, the author describes the development of the experimental diffraction setup and structural analysis of non-crystalline particles from material science and biology. Recent advances in X-ray free electron laser (XFEL)-coherent X-ray diffraction imaging (CXDI) experiments allow for the structural analysis of non-crystalline particles to a resolution of 7 nm, and to a resolution of 20 nm for biological materials. Now XFEL-CXDI marks the dawn of a new era in structural analys of non-crystalline particles with dimensions larger than 100 nm, which was quite impossible in the 20th century. To conduct CXDI experiments in both synchrotron and XFEL facilities, the author has developed apparatuses, named KOTOBUKI-1 and TAKASAGO-6 for cryogenic diffraction experiments on frozen-hydrated non-crystalline particles at around 66 K. At the synchrotron facility, cryogenic diffraction experiments dramatically reduce radiation damage of specimen particles and allow tomography CXDI experiments. In addition, in XFEL ex...

  12. [Radar as imaging tool in ecology and conservation biology].

    Science.gov (United States)

    Matyjasiak, Piotr

    2017-01-01

    Migrations and dispersal are among the most important ecological processes that shape ecosystems and influence our economy, health and safety. Movements of birds, bats and insects occur in a large spatial scale - regional, continental, or intercontinental. However, studies of these phenomena using classic methods are usually local. Breakthrough came with the development of radar technology, which enabled researchers to study animal movements in the atmosphere in a large spatial and temporal scale. The aim of this article was to present the radar imaging methods used in the research of aerial movements of birds, bats and insects. The types of radars used in research are described, and examples of the use of radar in basic research and in conservation biology are discussed. Radar visualizations are used in studies on the effect of meteorological conditions on bird migration, on spatial and temporal dynamics of movements of birds, bats and insects, and on the mechanism of orientation of migrating birds and insects. In conservation biology research radars are used in the monitoring of endangered species of birds and bats, to monitor bird activity at airports, as well as in assessing the impact of high constructions on flying birds and bats.

  13. An Integrated Biological Control System At Hanford

    International Nuclear Information System (INIS)

    Johnson, A.R.; Caudill, J.G.; Giddings, R.F.; Rodriguez, J.M.; Roos, R.C.; Wilde, J.W.

    2010-01-01

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimate spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  14. AN INTEGRATED BIOLOGICAL CONTROL SYSTEM AT HANFORD

    Energy Technology Data Exchange (ETDEWEB)

    JOHNSON AR; CAUDILL JG; GIDDINGS RF; RODRIGUEZ JM; ROOS RC; WILDE JW

    2010-02-11

    In 1999 an integrated biological control system was instituted at the U.S. Department of Energy's Hanford Site. Successes and changes to the program needed to be communicated to a large and diverse mix of organizations and individuals. Efforts at communication are directed toward the following: Hanford Contractors (Liquid or Tank Waste, Solid Waste, Environmental Restoration, Science and Technology, Site Infrastructure), General Hanford Employees, and Hanford Advisory Board (Native American Tribes, Environmental Groups, Local Citizens, Washington State and Oregon State regulatory agencies). Communication was done through direct interface meetings, individual communication, where appropriate, and broadly sharing program reports. The objectives of the communication efforts was to have the program well coordinated with Hanford contractors, and to have the program understood well enough that all stakeholders would have confidence in the work performed by the program to reduce or elimated spread of radioactive contamination by biotic vectors. Communication of successes and changes to an integrated biological control system instituted in 1999 at the Department of Energy's Hanford Site have required regular interfaces with not only a diverse group of Hanford contractors (i.e., those responsible for liquid or tank waste, solid wastes, environmental restoration, science and technology, and site infrastructure), and general Hanford employees, but also with a consortium of designated stake holders organized as the Hanford Advisory Board (i.e., Native American tribes, various environmental groups, local citizens, Washington state and Oregon regulatory agencies, etc.). Direct interface meetings, individual communication where appropriate, and transparency of the biological control program were the methods and outcome of this effort.

  15. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  16. Stochastic transport processes in discrete biological systems

    CERN Document Server

    Frehland, Eckart

    1982-01-01

    These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re­ cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio­ logical 'transport systems can be complex. For example, the tr...

  17. Model checking biological systems described using ambient calculus

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Priami, Corrado; Qualia, Paola

    2005-01-01

    Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005.......Model checking biological systems described using ambient calculus. In Proc. of the second International Workshop on Computational Methods in Systems Biology (CMSB04), Lecture Notes in Bioinformatics 3082:85-103, Springer, 2005....

  18. Calculating life? Duelling discourses in interdisciplinary systems biology.

    Science.gov (United States)

    Calvert, Jane; Fujimura, Joan H

    2011-06-01

    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

  19. Interactions of nanomaterials and biological systems: implications to personalized nanomedicine☆

    Science.gov (United States)

    Zhang, Xue-Qing; Xu, Xiaoyang; Bertrand, Nicolas; Pridgen, Eric; Swami, Archana; Farokhzad, Omid C.

    2012-01-01

    The application of nanotechnology to personalized medicine provides an unprecedented opportunity to improve the treatment of many diseases. Nanomaterials offer several advantages as therapeutic and diagnostic tools due to design flexibility, small sizes, large surface-to-volume ratio, and ease of surface modification with multivalent ligands to increase avidity for target molecules. Nanomaterials can be engineered to interact with specific biological components, allowing them to benefit from the insights provided by personalized medicine techniques. To tailor these interactions, a comprehensive knowledge of how nanomaterials interact with biological systems is critical. Herein, we discuss how the interactions of nanomaterials with biological systems can guide their design for diagnostic, imaging and drug delivery purposes. A general overview of nanomaterials under investigation is provided with an emphasis on systems that have reached clinical trials. Finally, considerations for the development of personalized nanomedicines are summarized such as the potential toxicity, scientific and technical challenges in fabricating them, and regulatory and ethical issues raised by the utilization of nanomaterials. PMID:22917779

  20. Microbial stress tolerance for biofuels. Systems biology

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zonglin Lewis (ed.) [National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL (United States)

    2012-07-01

    The development of sustainable and renewable biofuels is attracting growing interest. It is vital to develop robust microbial strains for biocatalysts that are able to function under multiple stress conditions. This Microbiology Monograph provides an overview of methods for studying microbial stress tolerance for biofuels applications using a systems biology approach. Topics covered range from mechanisms to methodology for yeast and bacteria, including the genomics of yeast tolerance and detoxification; genetics and regulation of glycogen and trehalose metabolism; programmed cell death; high gravity fermentations; ethanol tolerance; improving biomass sugar utilization by engineered Saccharomyces; the genomics on tolerance of Zymomonas mobilis; microbial solvent tolerance; control of stress tolerance in bacterial host organisms; metabolomics for ethanologenic yeast; automated proteomics work cell systems for strain improvement; and unification of gene expression data for comparable analyses under stress conditions. (orig.)

  1. Spatial Structures and Regulation in Biological Systems

    DEFF Research Database (Denmark)

    Yde, Pernille

    , and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider...... a previously studied and very general aggregation model describing frangible linear filaments. This model is especially relevant for the growth of amyloid fibres, that have been related to a number of serious human diseases, and which are known to grow in an accelerated self-enhanced manner.We derive...... model of the tissue and show how coupled cells are able to function as an excitable medium and propagate waves of high cytokine concentration through the tissue. If the internal regulation in the cells is over-productive, the model predicts a continuous amplification of cytokines, which spans the entire...

  2. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  3. Intellectual system for images restoration

    Science.gov (United States)

    Mardare, Igor

    2005-02-01

    Intelligence systems on basis of artificial neural networks and associative memory allow to solve effectively problems of recognition and restoration of images. However, within analytical technologies there are no dominating approaches of deciding of intellectual problems. Choice of the best technology depends on nature of problem, features of objects, volume of represented information about the object, number of classes of objects, etc. It is required to determine opportunities, preconditions and field of application of neural networks and associative memory for decision of problem of restoration of images and to use their supplementary benefits for further development of intelligence systems.

  4. Biologic targets identified from dynamic 18FDG-PET and implications for image-guided therapy

    International Nuclear Information System (INIS)

    Rusten, Espen; Malinen, Eirik; Roedal, Jan; Bruland, Oeyvind S.

    2013-01-01

    Purpose: The outcome of biologic image-guided radiotherapy depends on the definition of the biologic target. The purpose of the current work was to extract hyper perfused and hypermetabolic regions from dynamic positron emission tomography (D-PET) images, to dose escalate either region and to discuss implications of such image guided strategies. Methods: Eleven patients with soft tissue sarcomas were investigated with D-PET. The images were analyzed using a two-compartment model producing parametric maps of perfusion and metabolic rate. The two image series were segmented and exported to a treatment planning system, and biological target volumes BTV per and BTV met (perfusion and metabolism, respectively) were generated. Dice's similarity coefficient was used to compare the two biologic targets. Intensity-modulated radiation therapy (IMRT) plans were generated for a dose painting by contours regime, where planning target volume (PTV) was planned to 60 Gy and BTV to 70 Gy. Thus, two separate plans were created for each patient with dose escalation of either BTV per or BTV met . Results: BTV per was somewhat smaller than BTV met (209 ±170 cm 3 against 243 ±143 cm 3 , respectively; population-based mean and s.d.). Dice's coefficient depended on the applied margin, and was 0.72 ±0.10 for a margin of 10 mm. Boosting BTV per resulted in mean dose of 69 ±1.0 Gy to this region, while BTV met received 67 ±3.2 Gy. Boosting BTV met gave smaller dose differences between the respective non-boost DVHs (such as D 98 ). Conclusions: Dose escalation of one of the BTVs results in a partial dose escalation of the other BTV as well. If tumor aggressiveness is equally pronounced in hyper perfused and hypermetabolic regions, this should be taken into account in the treatment planning

  5. The Groningen image processing system

    International Nuclear Information System (INIS)

    Allen, R.J.; Ekers, R.D.; Terlouw, J.P.

    1985-01-01

    This paper describes an interactive, integrated software and hardware computer system for the reduction and analysis of astronomical images. A short historical introduction is presented before some examples of the astonomical data currently handled by the system are shown. A description is given of the present hardware and software structure. The system is illustrated by describing its appearance to the user, to the applications programmer, and to the system manager. Some quantitative information on the size and cost of the system is given, and its good and bad features are discussed

  6. Musashi dynamic image processing system

    International Nuclear Information System (INIS)

    Murata, Yutaka; Mochiki, Koh-ichi; Taguchi, Akira

    1992-01-01

    In order to produce transmitted neutron dynamic images using neutron radiography, a real time system called Musashi dynamic image processing system (MDIPS) was developed to collect, process, display and record image data. The block diagram of the MDIPS is shown. The system consists of a highly sensitive, high resolution TV camera driven by a custom-made scanner, a TV camera deflection controller for optimal scanning, which adjusts to the luminous intensity and the moving speed of an object, a real-time corrector to perform the real time correction of dark current, shading distortion and field intensity fluctuation, a real time filter for increasing the image signal to noise ratio, a video recording unit and a pseudocolor monitor to realize recording in commercially available products and monitoring by means of the CRTs in standard TV scanning, respectively. The TV camera and the TV camera deflection controller utilized for producing still images can be applied to this case. The block diagram of the real-time corrector is shown. Its performance is explained. Linear filters and ranked order filters were developed. (K.I.)

  7. On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

    Science.gov (United States)

    Gomez-Ramirez, Jaime; Sanz, Ricardo

    2013-09-01

    One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Scanning Terahertz Heterodyne Imaging Systems

    Science.gov (United States)

    Siegel, Peter; Dengler, Robert

    2007-01-01

    Scanning terahertz heterodyne imaging systems are now at an early stage of development. In a basic scanning terahertz heterodyne imaging system, (see Figure 1) two far-infrared lasers generate beams denoted the local-oscillator (LO) and signal that differ in frequency by an amount, denoted the intermediate frequency (IF), chosen to suit the application. The LO beam is sent directly to a mixer as one of two inputs. The signal beam is focused to a spot on or in the specimen. After transmission through or reflection from the specimen, the beams are focused to a spot on a terahertz mixer, which extracts the IF outputs. The specimen is mounted on a translation stage, by means of which the focal spot is scanned across the specimen to build up an image.

  9. 3D Backscatter Imaging System

    Science.gov (United States)

    Whitaker, Ross (Inventor); Turner, D. Clark (Inventor)

    2016-01-01

    Systems and methods for imaging an object using backscattered radiation are described. The imaging system comprises both a radiation source for irradiating an object that is rotationally movable about the object, and a detector for detecting backscattered radiation from the object that can be disposed on substantially the same side of the object as the source and which can be rotationally movable about the object. The detector can be separated into multiple detector segments with each segment having a single line of sight projection through the object and so detects radiation along that line of sight. Thus, each detector segment can isolate the desired component of the backscattered radiation. By moving independently of each other about the object, the source and detector can collect multiple images of the object at different angles of rotation and generate a three dimensional reconstruction of the object. Other embodiments are described.

  10. Notions of similarity for systems biology models.

    Science.gov (United States)

    Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar

    2018-01-01

    Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases. © The Author 2016. Published by Oxford University Press.

  11. Hydrogen production from biomass by biological systems

    International Nuclear Information System (INIS)

    Sharifan, H.R.; Qader, S.

    2009-01-01

    Hydrogen gas is seen as a future energy carrier, not involved in 'greenhouse' gas and its released energy in combustion can be converted to electric power. Biological system with low energy can produce hydrogen compared to electrochemical hydrogen production via solar battery-based water splitting which requires the use of solar batteries with high energy requirements. The biological hydrogen production occurs in microalgae and cyanobacteria by photosynthesis. They consume biochemical energy to produce molecular hydrogen. Hydrogen in some algae is an anaerobic production in the absence of light. In cyanobacteria the hydrogen production simultaneously happens with nitrogen fixation, and also catalyzed by nitrogenase as a side reaction. Hydrogen production by photosynthetic bacteria is mediated by nitrogenase activity, although hydrogenases may be active for both hydrogen production and hydrogen uptake under some conditions. Genetic studies on photosynthetic microorganisms have markedly increased in recent times, relatively few genetic engineering studies have focused on altering the characteristics of these microorganisms, particularly with respect to enhancing the hydrogen-producing capabilities of photosynthetic bacteria and cyanobacteria. (author)

  12. Image reconstruction of dynamic infrared single-pixel imaging system

    Science.gov (United States)

    Tong, Qi; Jiang, Yilin; Wang, Haiyan; Guo, Limin

    2018-03-01

    Single-pixel imaging technique has recently received much attention. Most of the current single-pixel imaging is aimed at relatively static targets or the imaging system is fixed, which is limited by the number of measurements received through the single detector. In this paper, we proposed a novel dynamic compressive imaging method to solve the imaging problem, where exists imaging system motion behavior, for the infrared (IR) rosette scanning system. The relationship between adjacent target images and scene is analyzed under different system movement scenarios. These relationships are used to build dynamic compressive imaging models. Simulation results demonstrate that the proposed method can improve the reconstruction quality of IR image and enhance the contrast between the target and the background in the presence of system movement.

  13. 3S - Systematic, systemic, and systems biology and toxicology.

    Science.gov (United States)

    Smirnova, Lena; Kleinstreuer, Nicole; Corvi, Raffaella; Levchenko, Andre; Fitzpatrick, Suzanne C; Hartung, Thomas

    2018-01-01

    A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

  14. Imaging Systems in TLE Research

    DEFF Research Database (Denmark)

    Allin, Thomas Højgaard; Neubert, Torsten; Laursen, Steen

    2006-01-01

    documented using the right equipment in the right way. This chapter provides an introduction to the concepts of low light imagers, and how they can be successfully applied in TLE research. As examples, we describe the 2003 and 2004 Spritewatch systems, which integrate low-light cameras with a digital...

  15. Computational Modeling of Biological Systems From Molecules to Pathways

    CERN Document Server

    2012-01-01

    Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

  16. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-01-01

    Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched

  17. Hologenomics: Systems-Level Host Biology.

    Science.gov (United States)

    Theis, Kevin R

    2018-01-01

    The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.

  18. Biomarkers of Nanoparticles Impact on Biological Systems

    Science.gov (United States)

    Mikhailenko, V.; Ieleiko, L.; Glavin, A.; Sorochinska, J.

    Studies of nanoscale mineral fibers have demonstrated that the toxic and carcinogenic effects are related to the surface area and surface activity of inhaled particles. Particle surface characteristics are considered to be key factors in the generation of free radicals and reactive oxygen species and are related to the development of apoptosis or cancer. Existing physico-chemical methods do not always allow estimation of the nanoparticles impact on organismal and cellular levels. The aim of this study was to develop marker system for evaluation the toxic and carcinogenic effects of nanoparticles on cells. The markers are designed with respect to important nanoparticles characteristics for specific and sensitive assessment of their impact on biological system. We have studied DNA damage, the activity of xanthine oxidoreductase influencing the level of free radicals, bioenergetic status, phospholipids profile and formation of 1H-NMR-visible mobile lipid domains in Ehrlich carcinoma cells. The efficiency of the proposed marker system was tested in vivo and in vitro with the use of C60 fullerene nanoparticles and multiwalled carbon nanotubes. Our data suggest that multiwalled carbon nanotubes and fullerene C60 may pose genotoxic effect, change energy metabolism and membrane structure, alter free radical level via xanthine oxidase activation and cause mobile lipid domains formation as determined in vivo and in vitro studies on Ehrlich carcinoma cells.

  19. Imaging systems for medical diagnostics

    International Nuclear Information System (INIS)

    Krestel, E.

    1990-01-01

    This book provides physicians and clinical physicists with detailed information on today's imaging modalities and assists them in selecting the optimal system for each clinical application. Physicists, engineers and computer specialists engaged in research and development and sales departments will also find this book to be of considerable use. It may also be employed at universities, training centers and in technical seminars. The physiological and physical fundamentals are explained in part 1. The technical solutions contained in part 2 illustrate the numerous possibilities available in X-ray diagnostics, computed tomography, nuclear medical diagnostics, magnetic resonance imaging, sonography and biomagnetic diagnostics. (orig.)

  20. Systems Biology of Metabolism: Annual Review of Biochemistry

    DEFF Research Database (Denmark)

    Nielsen, Jens

    2017-01-01

    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

  1. Imaging systems in nuclear medicine and image evaluation

    International Nuclear Information System (INIS)

    Beck, R.; Charleston, D.; Metz, C.

    1980-01-01

    This project deals with imaging systems in nuclear medicine and image evaluation and is presented as four subprojects. The goal of the first subproject is to improve diagnositc image quality by development of a general computer code for optimizing collimator design. The second subproject deals with a secondary emission and fluorescence technique for thyroid scanning while the third subproject emphasizes the need for more sophisticated image processing systems such as coherent optical spatial filtering systems and digital image processing. The fourth subproject presents a new approach for processing image data by taking into account the energy of each detected gamma-ray photon

  2. Multispectral Panoramic Imaging System, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — International Electronic Machines Corporation, a leader in the design of precision imaging systems, will develop an innovative multispectral, panoramic imaging...

  3. A SYSTEMIC VISION OF BIOLOGY: OVERCOMING LINEARITY

    Directory of Open Access Journals (Sweden)

    M. Mayer

    2005-07-01

    Full Text Available Many  authors have proposed  that contextualization of reality  is necessary  to teach  Biology, empha- sizing students´ social and  economic realities.   However, contextualization means  more than  this;  it is related  to working with  different kinds of phenomena  and/or objects  which enable  the  expression of scientific concepts.  Thus,  contextualization allows the integration of different contents.  Under this perspective,  the  objectives  of this  work were to articulate different  biology concepts  in order  to de- velop a systemic vision of biology; to establish  relationships with other areas of knowledge and to make concrete the  cell molecular  structure and organization as well as their  implications  on living beings´ environment, using  contextualization.  The  methodology  adopted  in this  work  was based  on three aspects:  interdisciplinarity, contextualization and development of competences,  using energy:  its flux and transformations as a thematic axis and  an approach  which allowed the  interconnection between different situations involving  these  concepts.   The  activities developed  were:  1.   dialectic exercise, involving a movement around  micro and macroscopic aspects,  by using questions  and activities,  sup- ported  by the use of alternative material  (as springs, candles on the energy, its forms, transformations and  implications  in the  biological way (microscopic  concepts;  2, Construction of molecular  models, approaching the concepts of atom,  chemical bonds and bond energy in molecules; 3. Observations de- veloped in Manguezal¨(mangrove swamp  ecosystem (Itapissuma, PE  were used to work macroscopic concepts  (as  diversity  and  classification  of plants  and  animals,  concerning  to  energy  flow through food chains and webs. A photograph register of all activities  along the course plus texts

  4. Designer genes. Recombinant antibody fragments for biological imaging

    Energy Technology Data Exchange (ETDEWEB)

    Wu, A.M.; Yazaki, P.J. [Beckman Research Institute of the City of Hope, Duarte, CA (United States). Dept. of Molecular Biology

    2000-09-01

    and expression, combined with novel specificities that will arise form advances in genomic and combinatorial approaches to target discovery, will usher in a new era of recombinant antibodies for biological imaging.

  5. Designer genes. Recombinant antibody fragments for biological imaging

    International Nuclear Information System (INIS)

    Wu, A.M.; Yazaki, P.J.

    2000-01-01

    expression, combined with novel specificities that will arise form advances in genomic and combinatorial approaches to target discovery, will usher in a new era of recombinant antibodies for biological imaging

  6. Ecological and biological systems under extreme conditions

    Energy Technology Data Exchange (ETDEWEB)

    Zlobin, V S; Nenishkiene, V B

    1989-01-01

    The behaviour of biological and ecological systems under extreme conditions (high and low temperatures, electromagnetic fields of different frequencies, ultraviolet. X-ray and gamma radiation) is analyzed. The ecosystems of macro- and microalgae living in salt, brackinsh and fresh waters are considered in the evolutional aspect basing on their chemical and biochemical composition taking into account the mechanism of radionuclide uptake by water plant cells, osmotic regulation, water and ice structures, combined water in a living organism. The problems of life-support in cosmic flights and of mastering the planets of the Solar system, for instance Mars and Venus, utilizing some microalgae and bacteria with high adaptive properties are discussed. Abnormal water points and their role in the metabolism of a water plant cell are estimated. The 'life niches' are determined at the temperatures exceeding 100 deg C and the possibility of existence for living organisms in high pressure and temperature is grounded. Attempts are made to change the metabolism of the plant and animal cell by subjecting it to the action of electromagnetic and thermal fields, heavy water, chemical and pharmocological substances changing the structure of bound water. 333 refs.; 79 tabs.

  7. Complexity, Analysis and Control of Singular Biological Systems

    CERN Document Server

    Zhang, Qingling; Zhang, Xue

    2012-01-01

    Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

  8. Network Reconstruction of Dynamic Biological Systems

    OpenAIRE

    Asadi, Behrang

    2013-01-01

    Inference of network topology from experimental data is a central endeavor in biology, since knowledge of the underlying signaling mechanisms a requirement for understanding biological phenomena. As one of the most important tools in bioinformatics area, development of methods to reconstruct biological networks has attracted remarkable attention in the current decade. Integration of different data types can lead to remarkable improvements in our ability to identify the connectivity of differe...

  9. New tools for redox biology: From imaging to manipulation.

    Science.gov (United States)

    Bilan, Dmitry S; Belousov, Vsevolod V

    2017-08-01

    Redox reactions play a key role in maintaining essential biological processes. Deviations in redox pathways result in the development of various pathologies at cellular and organismal levels. Until recently, studies on transformations in the intracellular redox state have been significantly hampered in living systems. The genetically encoded indicators, based on fluorescent proteins, have provided new opportunities in biomedical research. The existing indicators already enable monitoring of cellular redox parameters in different processes including embryogenesis, aging, inflammation, tissue regeneration, and pathogenesis of various diseases. In this review, we summarize information about all genetically encoded redox indicators developed to date. We provide the description of each indicator and discuss its advantages and limitations, as well as points that need to be considered when choosing an indicator for a particular experiment. One chapter is devoted to the important discoveries that have been made by using genetically encoded redox indicators. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Systems biology of microbial exopolysaccharides production

    Directory of Open Access Journals (Sweden)

    Ozlem eAtes

    2015-12-01

    Full Text Available Exopolysaccharides (EPS produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture and medicine. EPSs are mainly associated with high-value applications and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore a systems-based approach constitutes an important step towards understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan and dextran.

  11. Systems Biology of Microbial Exopolysaccharides Production.

    Science.gov (United States)

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

  12. Imaging systems and materials characterization

    International Nuclear Information System (INIS)

    Murr, L.E.

    2009-01-01

    This paper provides a broad background for the historical development and modern applications of light optical metallography, scanning and transmission electron microscopy, field-ion microscopy and several forms of scanning probe microscopes. Numerous case examples illustrating especially synergistic applications of these imaging systems are provided to demonstrate materials characterization especially in the context of structure-property-performance issues which define materials science and engineering

  13. GEOREFERENCED IMAGE SYSTEM WITH DRONES

    Directory of Open Access Journals (Sweden)

    Héctor A. Pérez-Sánchez

    2017-07-01

    Full Text Available This paper has as general purpose develop and implementation of a system that allows the generation of flight routes for a drone, the acquisition of geographic location information (GPS during the flight and taking photographs of points of interest for creating georeferenced images, same that will be used to generate KML files (Keyhole Markup Language for the representation of geographical data in three dimensions to be displayed on the Google Earth tool.

  14. Application of blue-green and ultraviolet micro-LEDs to biological imaging and detection

    International Nuclear Information System (INIS)

    Xu, H; Zhang, J; Nurmikko, A V; Davitt, K M; Song, Y-K

    2008-01-01

    This paper reviews authors' laboratory's work on the development of nitride-based blue-green and ultraviolet microscale LED devices with particular classes of imaging and spectroscopic applications in cellular level biology. Starting from neuroscience, we illustrate the utility of blue-green micro-LEDs for voltage-sensitive dye imaging of individual neural cells, as well as their ultraviolet counterparts for photostimulation of neurons. Arrays of micro-LEDs are also shown to be useful in projecting spatiotemporal patterns of photoexcitation to study the visual system development in living animals. As another illustration of the utility of the emerging nitride microdevice technology, we demonstrate the application of UV micro-LED arrays in bio-sensing technology as the core of a real-time fluorescence spectroscopy biowarning system. (invited paper)

  15. Molecular Imaging with Activatable Reporter Systems

    Directory of Open Access Journals (Sweden)

    Gang Niu, Xiaoyuan Chen

    2012-01-01

    Full Text Available Molecular imaging is a newly emerged multiple disciplinary field that aims to visualize, characterize and quantitatively measure biological processes at cellular and molecular levels in humans and other living systems. A reporter gene is a piece of DNA encoding reporter protein, which presents as a readily measurable phenotype that can be distinguished easily from the background of endogenous protein. After being transferred into cells of organ systems (transgenes, the reporter gene can be utilized to visualize transcriptional and posttranscriptional regulation of gene expression, protein-protein interactions, or trafficking of proteins or cells in living subjects. Herein, we review previous classification of reporter genes and regroup the reporter gene based imaging as basic, inducible and activatable, based on the regulation of reporter gene transcription and post-translational modification of reporter proteins. We then focus on activatable reporters, in which the signal can be activated at the posttranslational level for visualizing protein-protein interactions, protein phosphorylation or tertiary structure changes. The applications of several types of activatable reporters will also be summarized. We conclude that activatable reporter imaging can benefit both basic biomedical research and drug development.

  16. Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

    Science.gov (United States)

    Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

    2017-07-05

    Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Quantifying electron transfer reactions in biological systems

    DEFF Research Database (Denmark)

    Sjulstok, Emil Sjulstok; Olsen, Jógvan Magnus Haugaard; Solov'yov, Ilia A

    2015-01-01

    which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between...

  18. Systems biology: properties of reconstructed networks

    National Research Council Canada - National Science Library

    Palsson, Bernhard

    2006-01-01

    ... between the mathematical ideas and biological processes are made clear, the book reflects the irreversible trend of increasing mathematical content in biology education. Therefore to assist both teacher and student, Palsson provides problem sets, projects, and PowerPoint slides in an associated web site and keeps the presentation in the book concrete with illustrat...

  19. Precision medicine driven by cancer systems biology.

    Science.gov (United States)

    Filipp, Fabian V

    2017-03-01

    Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors. Mutation hotspots, structural modeling, UV signature, and genomic as well as non-genomic mechanisms of disease initiation and progression are taken into consideration to identify resistance mutations and novel drug targets. A comprehensive precision medicine profile of a malignant melanoma patient illustrates future rational drug targeting strategies. Network analysis emphasizes an important role of epigenetic and metabolic master regulators in oncogenesis. Co-occurrence of driver mutations in signaling, metabolic, and epigenetic factors highlights how cumulative alterations of our genomes and epigenomes progressively lead to uncontrolled cell proliferation. Precision insights have the ability to identify independent molecular pathways suitable for drug targeting. Synergistic treatment combinations of orthogonal modalities including immunotherapy, mitogen-activated protein kinase inhibitors, epigenetic inhibitors, and metabolic inhibitors have the potential to overcome immune evasion, side effects, and drug resistance.

  20. Isotopic fractionation of tritium in biological systems.

    Science.gov (United States)

    Le Goff, Pierre; Fromm, Michel; Vichot, Laurent; Badot, Pierre-Marie; Guétat, Philippe

    2014-04-01

    Isotopic fractionation of tritium is a highly relevant issue in radiation protection and requires certain radioecological considerations. Sound evaluation of this factor is indeed necessary to determine whether environmental compartments are enriched/depleted in tritium or if tritium is, on the contrary, isotopically well-distributed in a given system. The ubiquity of tritium and the standard analytical methods used to assay it may induce biases in both the measurement and the signification that is accorded to the so-called fractionation: based on an exhaustive review of the literature, we show how, sometimes large deviations may appear. It is shown that when comparing the non-exchangeable fraction of organically bound tritium (neOBT) to another fraction of tritium (e.g. tritiated water) the preparation of samples and the measurement of neOBT reported frequently led to underestimation of the ratio of tritium to hydrogen (T/H) in the non-exchangeable compartment by a factor of 5% to 50%. In the present study, corrections are proposed for most of the biological matrices studied so far. Nevertheless, the values of isotopic fractionation reported in the literature remain difficult to compare with each other, especially since the physical quantities and units often vary between authors. Some improvements are proposed to better define what should encompass the concepts of exchangeable and non-exchangeable fractions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Toward mechanical systems biology in bone.

    Science.gov (United States)

    Trüssel, Andreas; Müller, Ralph; Webster, Duncan

    2012-11-01

    Cyclic mechanical loading is perhaps the most important physiological factor regulating bone mass and shape in a way which balances optimal strength with minimal weight. This bone adaptation process spans multiple length and time scales. Forces resulting from physiological exercise at the organ scale are sensed at the cellular scale by osteocytes, which reside inside the bone matrix. Via biochemical pathways, osteocytes orchestrate the local remodeling action of osteoblasts (bone formation) and osteoclasts (bone resorption). Together these local adaptive remodeling activities sum up to strengthen bone globally at the organ scale. To resolve the underlying mechanisms it is required to identify and quantify both cause and effect across the different scales. Progress has been made at the different scales experimentally. Computational models of bone adaptation have been developed to piece together various experimental observations at the different scales into coherent and plausible mechanisms. However additional quantitative experimental validation is still required to build upon the insights which have already been achieved. In this review we discuss emerging as well as state of the art experimental and computational techniques and how they might be used in a mechanical systems biology approach to further our understanding of the mechanisms governing load induced bone adaptation, i.e., ways are outlined in which experimental and computational approaches could be coupled, in a quantitative manner to create more reliable multiscale models of bone.

  2. Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

    Science.gov (United States)

    2011-01-01

    Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

  3. SU-E-I-75: Development of New Biological Fingerprints for Patient Recognition to Identify Misfiled Images in a PACS Server

    International Nuclear Information System (INIS)

    Shimizu, Y; Yoon, Y; Iwase, K; Yasumatsu, S; Matsunobu, Y; Morishita, J

    2015-01-01

    Purpose: We are trying to develop an image-searching technique to identify misfiled images in a picture archiving and communication system (PACS) server by using five biological fingerprints: the whole lung field, cardiac shadow, superior mediastinum, lung apex, and right lower lung. Each biological fingerprint in a chest radiograph includes distinctive anatomical structures to identify misfiled images. The whole lung field was less effective for evaluating the similarity between two images than the other biological fingerprints. This was mainly due to the variation in the positioning for chest radiographs. The purpose of this study is to develop new biological fingerprints that could reduce influence of differences in the positioning for chest radiography. Methods: Two hundred patients were selected randomly from our database (36,212 patients). These patients had two images each (current and previous images). Current images were used as the misfiled images in this study. A circumscribed rectangular area of the lung and the upper half of the rectangle were selected automatically as new biological fingerprints. These biological fingerprints were matched to all previous images in the database. The degrees of similarity between the two images were calculated for the same and different patients. The usefulness of new the biological fingerprints for automated patient recognition was examined in terms of receiver operating characteristic (ROC) analysis. Results: Area under the ROC curves (AUCs) for the circumscribed rectangle of the lung, upper half of the rectangle, and whole lung field were 0.980, 0.994, and 0.950, respectively. The new biological fingerprints showed better performance in identifying the patients correctly than the whole lung field. Conclusion: We have developed new biological fingerprints: circumscribed rectangle of the lung and upper half of the rectangle. These new biological fingerprints would be useful for automated patient identification system

  4. SU-E-I-75: Development of New Biological Fingerprints for Patient Recognition to Identify Misfiled Images in a PACS Server

    Energy Technology Data Exchange (ETDEWEB)

    Shimizu, Y; Yoon, Y; Iwase, K; Yasumatsu, S; Matsunobu, Y [Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, JP (Japan); Morishita, J [Department of Health Sciences, Faculty of Medical Sciences, Kyushu University, Fukuoka, JP (Japan)

    2015-06-15

    Purpose: We are trying to develop an image-searching technique to identify misfiled images in a picture archiving and communication system (PACS) server by using five biological fingerprints: the whole lung field, cardiac shadow, superior mediastinum, lung apex, and right lower lung. Each biological fingerprint in a chest radiograph includes distinctive anatomical structures to identify misfiled images. The whole lung field was less effective for evaluating the similarity between two images than the other biological fingerprints. This was mainly due to the variation in the positioning for chest radiographs. The purpose of this study is to develop new biological fingerprints that could reduce influence of differences in the positioning for chest radiography. Methods: Two hundred patients were selected randomly from our database (36,212 patients). These patients had two images each (current and previous images). Current images were used as the misfiled images in this study. A circumscribed rectangular area of the lung and the upper half of the rectangle were selected automatically as new biological fingerprints. These biological fingerprints were matched to all previous images in the database. The degrees of similarity between the two images were calculated for the same and different patients. The usefulness of new the biological fingerprints for automated patient recognition was examined in terms of receiver operating characteristic (ROC) analysis. Results: Area under the ROC curves (AUCs) for the circumscribed rectangle of the lung, upper half of the rectangle, and whole lung field were 0.980, 0.994, and 0.950, respectively. The new biological fingerprints showed better performance in identifying the patients correctly than the whole lung field. Conclusion: We have developed new biological fingerprints: circumscribed rectangle of the lung and upper half of the rectangle. These new biological fingerprints would be useful for automated patient identification system

  5. Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

    Science.gov (United States)

    Degrazio, Dominick

    Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

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

    Energy Technology Data Exchange (ETDEWEB)

    Wu, J.S., E-mail: jinsong-wu@northwestern.edu [Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208 (United States); Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208 (United States); Kim, A.M. [Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 (United States); Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208 (United States); Bleher, R. [Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208 (United States); Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208 (United States); Myers, B.D. [Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208 (United States); Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208 (United States); Marvin, R.G. [Department of Chemistry, Northwestern University, Evanston, IL 60208 (United States); Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208 (United States); Inada, H.; Nakamura, K. [Hitachi High-Technologies Corporation, Ibaraki 312-8504 (Japan); Zhang, X.F. [Hitachi High Technologies America, Inc., 5960 Inglewood Drive, Pleasanton, California 94588 (United States); Roth, E. [Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208 (United States); Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208 (United States); Li, S.Y. [Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208 (United States); and others

    2013-05-15

    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. - Highlights: ► Applications of STEM in characterization of biological samples are demonstrated. ► Elemental analyses are performed by dual EDS and EELS. ► Both the surface and internal structure of cells can be studied simultaneously. ► The imaging contrast in low-dose cryo-STEM has been analyzed.

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

    International Nuclear Information System (INIS)

    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.

    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. - Highlights: ► Applications of STEM in characterization of biological samples are demonstrated. ► Elemental analyses are performed by dual EDS and EELS. ► Both the surface and internal structure of cells can be studied simultaneously. ► The imaging contrast in low-dose cryo-STEM has been analyzed

  8. Image and information management system

    Science.gov (United States)

    Robertson, Tina L. (Inventor); Raney, Michael C. (Inventor); Dougherty, Dennis M. (Inventor); Kent, Peter C. (Inventor); Brucker, Russell X. (Inventor); Lampert, Daryl A. (Inventor)

    2009-01-01

    A system and methods through which pictorial views of an object's configuration, arranged in a hierarchical fashion, are navigated by a person to establish a visual context within the configuration. The visual context is automatically translated by the system into a set of search parameters driving retrieval of structured data and content (images, documents, multimedia, etc.) associated with the specific context. The system places ''hot spots'', or actionable regions, on various portions of the pictorials representing the object. When a user interacts with an actionable region, a more detailed pictorial from the hierarchy is presented representing that portion of the object, along with real-time feedback in the form of a popup pane containing information about that region, and counts-by-type reflecting the number of items that are available within the system associated with the specific context and search filters established at that point in time.

  9. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Nielsen, Jens; Jewett, Michael Christopher

    2008-01-01

    in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

  10. 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.

  11. Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

    DEFF Research Database (Denmark)

    Green, Sara; Serban, Maria; Scholl, Raphael

    2018-01-01

    of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

  12. X-ray imaging system

    International Nuclear Information System (INIS)

    Houston, J.M.

    1980-01-01

    A novel, high-speed apparatus for use in X-ray computerised tomography is described in detail. It consists of a semi-circular array of X-ray sources, collimators and an ion chamber array for detection of the X-rays. The X-ray sources may be pulsed in salvos such that the corresponding detectors in the array are only illuminated by one source. The use of computer controlled salvos speeds up the image processing by at least a factor of two. The ion chamber array is designed to have a constant detection efficiency for varying angles of X-ray incidence. A detailed description of the detector construction and suggested gaseous fillings are given. It is claimed that the present tomographic system allows fast and accurate imaging of internal body organs and is insensitive to the blurring effects which motion of these organs tends to produce. (UK)

  13. Whole body imaging system mechanism

    International Nuclear Information System (INIS)

    Carman, R.W.; Doherty, E.J.

    1980-01-01

    A radioisotope scanning apparatus for use in nuclear medicine is described in detail. The apparatus enables the quantification and spatial location of the radioactivity in a body section of a patient to be determined with high sensitivity. It consists of an array of highly focussed collimators arranged such that adjacent collimators move in the same circumferential but opposite radial directions. The explicit movements of the gantry are described in detail and may be controlled by a general purpose computer. The use of highly focussed collimators allows both a reasonable solid angle of acceptance and also high target to background images; additionally, dual radionuclide pharmaceutical studies can be performed simultaneously. It is claimed that the high sensitivity of the system permits the early diagnosis of pathological changes and the images obtained show accurately the location and shape of physiological abnormalities. (U.K.)

  14. Seasonal allergic rhinitis and systems biology-oriented biomarker discovery

    NARCIS (Netherlands)

    Baars, E.W.; Nierop, A.F.M.; Savelkoul, H.F.J.

    2015-01-01

    There is an increasing interest in science and medicine in the systems approach. Instead of the reductionist approach that focuses on the physical and chemical properties of the individual components, systems biology aims to describe, understand, and explain from the complex biological systems

  15. Exploring lipids with nonlinear optical microscopy in multiple biological systems

    Science.gov (United States)

    Alfonso-Garcia, Alba

    Lipids are crucial biomolecules for the well being of humans. Altered lipid metabolism may give rise to a variety of diseases that affect organs from the cardiovascular to the central nervous system. A deeper understanding of lipid metabolic processes would spur medical research towards developing precise diagnostic tools, treatment methods, and preventive strategies for reducing the impact of lipid diseases. Lipid visualization remains a complex task because of the perturbative effect exerted by traditional biochemical assays and most fluorescence markers. Coherent Raman scattering (CRS) microscopy enables interrogation of biological samples with minimum disturbance, and is particularly well suited for label-free visualization of lipids, providing chemical specificity without compromising on spatial resolution. Hyperspectral imaging yields large datasets that benefit from tailored multivariate analysis. In this thesis, CRS microscopy was combined with Raman spectroscopy and other label-free nonlinear optical techniques to analyze lipid metabolism in multiple biological systems. We used nonlinear Raman techniques to characterize Meibum secretions in the progression of dry eye disease, where the lipid and protein contributions change in ratio and phase segregation. We employed similar tools to examine lipid droplets in mice livers aboard a spaceflight mission, which lose their retinol content contributing to the onset of nonalcoholic fatty-liver disease. We also focused on atherosclerosis, a disease that revolves around lipid-rich plaques in arterial walls. We examined the lipid content of macrophages, whose variable phenotype gives rise to contrasting healing and inflammatory activities. We also proposed new label-free markers, based on lifetime imaging, for macrophage phenotype, and to detect products of lipid oxidation. Cholesterol was also detected in hepatitis C virus infected cells, and in specific strains of age-related macular degeneration diseased cells by

  16. Breeding system and pollination biology of the semidomesticated ...

    African Journals Online (AJOL)

    Breeding system and pollination biology of the semidomesticated fruit tree, Tamarindus indica L. (Leguminosae: Caesalpinioideae ): Implications for fruit production, selective breeding, and conservation of genetic resources.

  17. Design of low noise imaging system

    Science.gov (United States)

    Hu, Bo; Chen, Xiaolai

    2017-10-01

    In order to meet the needs of engineering applications for low noise imaging system under the mode of global shutter, a complete imaging system is designed based on the SCMOS (Scientific CMOS) image sensor CIS2521F. The paper introduces hardware circuit and software system design. Based on the analysis of key indexes and technologies about the imaging system, the paper makes chips selection and decides SCMOS + FPGA+ DDRII+ Camera Link as processing architecture. Then it introduces the entire system workflow and power supply and distribution unit design. As for the software system, which consists of the SCMOS control module, image acquisition module, data cache control module and transmission control module, the paper designs in Verilog language and drives it to work properly based on Xilinx FPGA. The imaging experimental results show that the imaging system exhibits a 2560*2160 pixel resolution, has a maximum frame frequency of 50 fps. The imaging quality of the system satisfies the requirement of the index.

  18. Image BOSS: a biomedical object storage system

    Science.gov (United States)

    Stacy, Mahlon C.; Augustine, Kurt E.; Robb, Richard A.

    1997-05-01

    Researchers using biomedical images have data management needs which are oriented perpendicular to clinical PACS. The image BOSS system is designed to permit researchers to organize and select images based on research topic, image metadata, and a thumbnail of the image. Image information is captured from existing images in a Unix based filesystem, stored in an object oriented database, and presented to the user in a familiar laboratory notebook metaphor. In addition, the ImageBOSS is designed to provide an extensible infrastructure for future content-based queries directly on the images.

  19. Multi-channel medical imaging system

    Science.gov (United States)

    Frangioni, John V

    2013-12-31

    A medical imaging system provides simultaneous rendering of visible light and fluorescent images. The system may employ dyes in a small-molecule form that remain in the subject's blood stream for several minutes, allowing real-time imaging of the subject's circulatory system superimposed upon a conventional, visible light image of the subject. The system may provide an excitation light source to excite the fluorescent substance and a visible light source for general illumination within the same optical guide used to capture images. The system may be configured for use in open surgical procedures by providing an operating area that is closed to ambient light. The systems described herein provide two or more diagnostic imaging channels for capture of multiple, concurrent diagnostic images and may be used where a visible light image may be usefully supplemented by two or more images that are independently marked for functional interest.

  20. How do biological systems escape 'chaotic' state?

    Indian Academy of Sciences (India)

    B J Rao

    2018-02-13

    Feb 13, 2018 ... Lorencova 2016), sociology, physics, computer science, economics and even biology ... dynamic complexity associated with them at multiple levels? .... Social anthropology and the science of chaos (Oxford: Berghahn Books).

  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. Industrial systems biology and its impact on synthetic biology of yeast cell factories.

    Science.gov (United States)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-06-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  3. Industrial systems biology and its impact on synthetic biology of yeast cell factories

    DEFF Research Database (Denmark)

    Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

    2016-01-01

    Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

  4. New imaging systems in nuclear medicine

    International Nuclear Information System (INIS)

    1989-01-01

    PCR-I, an analog coded single ring positron tomograph, demonstrates the concepts of analog coding and the utility of high resolution systems. PCR-I, with a resolution of 4.5mm, has been employed in a series of biological studies using small animals that have been highly successful and will lead to clinical application. The emphasis now is turning to even higher sensitivity instruments in order to provide adequate number of events to populate a volume image. For this purpose, we have designed and are constructing PCR-II, a cylindrical analog coded positron tomograph incorporating 12,800 small detectors coded to 1760 phototubes. The increased sensitivity is achieved by recording all events within a cylindrical source that produce annihilation radiation striking any point on the cylindrical detector. PCR-II is projected to have a sensitivity of 1.6 million counts per second for a 20 centimeter diameter sphere uniformly filled with activity at 1 μCi/cm 3 . This system, with a resolution of 3mm, will approach the limits of sensitivity and resolution for positron tomographs. It is our opinion that this system will revolutionize the concept of positron imaging

  5. Raman imaging from microscopy to macroscopy: Quality and safety control of biological materials

    Science.gov (United States)

    Raman imaging can analyze biological materials by generating detailed chemical images. Over the last decade, tremendous advancements in Raman imaging and data analysis techniques have overcome problems such as long data acquisition and analysis times and poor sensitivity. This review article introdu...

  6. Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Mei Zhan

    2015-04-01

    Full Text Available Quantitative imaging has become a vital technique in biological discovery and clinical diagnostics; a plethora of tools have recently been developed to enable new and accelerated forms of biological investigation. Increasingly, the capacity for high-throughput experimentation provided by new imaging modalities, contrast techniques, microscopy tools, microfluidics and computer controlled systems shifts the experimental bottleneck from the level of physical manipulation and raw data collection to automated recognition and data processing. Yet, despite their broad importance, image analysis solutions to address these needs have been narrowly tailored. Here, we present a generalizable formulation for autonomous identification of specific biological structures that is applicable for many problems. The process flow architecture we present here utilizes standard image processing techniques and the multi-tiered application of classification models such as support vector machines (SVM. These low-level functions are readily available in a large array of image processing software packages and programming languages. Our framework is thus both easy to implement at the modular level and provides specific high-level architecture to guide the solution of more complicated image-processing problems. We demonstrate the utility of the classification routine by developing two specific classifiers as a toolset for automation and cell identification in the model organism Caenorhabditis elegans. To serve a common need for automated high-resolution imaging and behavior applications in the C. elegans research community, we contribute a ready-to-use classifier for the identification of the head of the animal under bright field imaging. Furthermore, we extend our framework to address the pervasive problem of cell-specific identification under fluorescent imaging, which is critical for biological investigation in multicellular organisms or tissues. Using these examples as a

  7. Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans.

    Science.gov (United States)

    Zhan, Mei; Crane, Matthew M; Entchev, Eugeni V; Caballero, Antonio; Fernandes de Abreu, Diana Andrea; Ch'ng, QueeLim; Lu, Hang

    2015-04-01

    Quantitative imaging has become a vital technique in biological discovery and clinical diagnostics; a plethora of tools have recently been developed to enable new and accelerated forms of biological investigation. Increasingly, the capacity for high-throughput experimentation provided by new imaging modalities, contrast techniques, microscopy tools, microfluidics and computer controlled systems shifts the experimental bottleneck from the level of physical manipulation and raw data collection to automated recognition and data processing. Yet, despite their broad importance, image analysis solutions to address these needs have been narrowly tailored. Here, we present a generalizable formulation for autonomous identification of specific biological structures that is applicable for many problems. The process flow architecture we present here utilizes standard image processing techniques and the multi-tiered application of classification models such as support vector machines (SVM). These low-level functions are readily available in a large array of image processing software packages and programming languages. Our framework is thus both easy to implement at the modular level and provides specific high-level architecture to guide the solution of more complicated image-processing problems. We demonstrate the utility of the classification routine by developing two specific classifiers as a toolset for automation and cell identification in the model organism Caenorhabditis elegans. To serve a common need for automated high-resolution imaging and behavior applications in the C. elegans research community, we contribute a ready-to-use classifier for the identification of the head of the animal under bright field imaging. Furthermore, we extend our framework to address the pervasive problem of cell-specific identification under fluorescent imaging, which is critical for biological investigation in multicellular organisms or tissues. Using these examples as a guide, we envision

  8. A Magnetic Sensor System for Biological Detection

    KAUST Repository

    Li, Fuquan

    2015-05-01

    Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched between a bio-functionalized sensor surface and bio-functionalized magnetic beads. This method has been used very successfully in different application, but its execution requires a rather elaborate procedure including several washing and incubation steps. This dissertation investigates a new magnetic biosensor concept, which enables a simple and effective detection of biological targets. The biosensor takes advantage of the size difference between bare magnetic beads and compounds of magnetic beads and biological targets. First, the detection of super-paramagnetic beads via magnetic tunnel junction (MTJ) sensors is implemented. Frequency modulation is used to enhance the signal-to-noise ratio, enabling the detection of a single magnetic bead. Second, the concept of the magnetic biosensor is investigated theoretically. The biosensor consists of an MTJ sensor, which detects the stray field of magnetic beads inside of a trap on top of the MTJ. A microwire between the trap and the MTJ is used to attract magnetic beads to the trapping well by applying a current to it. The MTJ sensor’s output depends on the number of beads inside the trap. If biological targets are in the sample solution, the beads will form bead compounds consisting of beads linked to the biological targets. Since bead compounds are larger than bare beads, the number of beads inside the trapping well will depend on the presence of biological targets. Hence, the output of the MTJ sensor will depend on the biological targets. The dependences of sensor signals on the sizes of the MTJ sensor, magnetic beads and biological targets are studied to find the optimum constellations for the detection of specific biological targets. The optimization is demonstrated

  9. Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery.

    Science.gov (United States)

    Simm, Jaak; Klambauer, Günter; Arany, Adam; Steijaert, Marvin; Wegner, Jörg Kurt; Gustin, Emmanuel; Chupakhin, Vladimir; Chong, Yolanda T; Vialard, Jorge; Buijnsters, Peter; Velter, Ingrid; Vapirev, Alexander; Singh, Shantanu; Carpenter, Anne E; Wuyts, Roel; Hochreiter, Sepp; Moreau, Yves; Ceulemans, Hugo

    2018-05-17

    In both academia and the pharmaceutical industry, large-scale assays for drug discovery are expensive and often impractical, particularly for the increasingly important physiologically relevant model systems that require primary cells, organoids, whole organisms, or expensive or rare reagents. We hypothesized that data from a single high-throughput imaging assay can be repurposed to predict the biological activity of compounds in other assays, even those targeting alternate pathways or biological processes. Indeed, quantitative information extracted from a three-channel microscopy-based screen for glucocorticoid receptor translocation was able to predict assay-specific biological activity in two ongoing drug discovery projects. In these projects, repurposing increased hit rates by 50- to 250-fold over that of the initial project assays while increasing the chemical structure diversity of the hits. Our results suggest that data from high-content screens are a rich source of information that can be used to predict and replace customized biological assays. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. The aims of systems biology: between molecules and organisms.

    Science.gov (United States)

    Noble, D

    2011-05-01

    The systems approach to biology has a long history. Its recent rapid resurgence at the turn of the century reflects the problems encountered in interpreting the sequencing of the genome and the failure of that immense achievement to provide rapid and direct solutions to major multi-factorial diseases. This paper argues that systems biology is necessarily multilevel and that there is no privileged level of causality in biological systems. It is an approach rather than a separate discipline. Functionality arises from biological networks that interact with the genome, the environment and the phenotype. This view of biology is very different from the gene-centred views of neo-Darwinism and molecular biology. In neuroscience, the systems approach leads naturally to 2 important conclusions: first, that the idea of 'programs' in the brain is confusing, and second, that the self is better interpreted as a process than as an object. © Georg Thieme Verlag KG Stuttgart · New York.

  11. 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.

  12. Hierarchical structure of biological systems: a bioengineering approach.

    Science.gov (United States)

    Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M

    2014-01-01

    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems.

  13. On the interplay between mathematics and biology: hallmarks toward a new systems biology.

    Science.gov (United States)

    Bellomo, Nicola; Elaiw, Ahmed; Althiabi, Abdullah M; Alghamdi, Mohammed Ali

    2015-03-01

    This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Probing the potential of neutron imaging for biomedical and biological applications

    International Nuclear Information System (INIS)

    Watkin, Kenneth L.; Bilheux, Hassina Z.; Ankner, John Francis

    2009-01-01

    Neutron imaging of biological specimens began soon after the discovery of the neutron by Chadwick in 1932. The first samples included tumors in tissues, internal organs in rats, and bones. These studies mainly employed thermal neutrons and were often compared with X-ray images of the same or equivalent samples. Although neutron scattering is widely used in biological studies, neutron imaging has yet to be exploited to its full capability in this area. This chapter summarizes past and current research efforts to apply neutron radiography to the study of biological specimens, in the expectation that clinical and medical research, as well as forensic science, may benefit from it.

  15. Automated, feature-based image alignment for high-resolution imaging mass spectrometry of large biological samples

    NARCIS (Netherlands)

    Broersen, A.; Liere, van R.; Altelaar, A.F.M.; Heeren, R.M.A.; McDonnell, L.A.

    2008-01-01

    High-resolution imaging mass spectrometry of large biological samples is the goal of several research groups. In mosaic imaging, the most common method, the large sample is divided into a mosaic of small areas that are then analyzed with high resolution. Here we present an automated alignment

  16. High dynamic range coding imaging system

    Science.gov (United States)

    Wu, Renfan; Huang, Yifan; Hou, Guangqi

    2014-10-01

    We present a high dynamic range (HDR) imaging system design scheme based on coded aperture technique. This scheme can help us obtain HDR images which have extended depth of field. We adopt Sparse coding algorithm to design coded patterns. Then we utilize the sensor unit to acquire coded images under different exposure settings. With the guide of the multiple exposure parameters, a series of low dynamic range (LDR) coded images are reconstructed. We use some existing algorithms to fuse and display a HDR image by those LDR images. We build an optical simulation model and get some simulation images to verify the novel system.

  17. Programming Morphogenesis through Systems and Synthetic Biology.

    Science.gov (United States)

    Velazquez, Jeremy J; Su, Emily; Cahan, Patrick; Ebrahimkhani, Mo R

    2018-04-01

    Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Improved Interactive Medical-Imaging System

    Science.gov (United States)

    Ross, Muriel D.; Twombly, Ian A.; Senger, Steven

    2003-01-01

    An improved computational-simulation system for interactive medical imaging has been invented. The system displays high-resolution, three-dimensional-appearing images of anatomical objects based on data acquired by such techniques as computed tomography (CT) and magnetic-resonance imaging (MRI). The system enables users to manipulate the data to obtain a variety of views for example, to display cross sections in specified planes or to rotate images about specified axes. Relative to prior such systems, this system offers enhanced capabilities for synthesizing images of surgical cuts and for collaboration by users at multiple, remote computing sites.

  19. Network science of biological systems at different scales: A review

    Science.gov (United States)

    Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

    2018-03-01

    Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

  20. SEEK: a systems biology data and model management platform.

    NARCIS (Netherlands)

    Wolstencroft, K.J.; Owen, S.; Krebs, O.; Nguyen, Q.; Stanford, N.J.; Golebiewski, M.; Weidemann, A.; Bittkowski, M.; An, L.; Shockley, D.; Snoep, J.L.; Mueller, W.; Goble, C.

    2015-01-01

    Background: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems

  1. Plant Systems Biology at the Single-Cell Level.

    Science.gov (United States)

    Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

    2017-11-01

    Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Imaging systems in nuclear medicine and image evaluation

    International Nuclear Information System (INIS)

    Beck, R.; Charleston, D.; Metz, C.; Tsui, B.

    1981-01-01

    A general computer code to simulate the imaging properties of existing and hypothetical imaging systems viewing realistic source distributions within non-uniform media. Such a code allows comparative evaluations of existing and hypothetical systems, and optimization of critical parameters of system design by maximizing the signal-to-noise ratio. To be most useful, such a code allows simulation of conventional scintillation scanners and cameras as well as single-photon and position tomographic systems

  3. Imaging system for creating 3D block-face cryo-images of whole mice

    Science.gov (United States)

    Roy, Debashish; Breen, Michael; Salvado, Olivier; Heinzel, Meredith; McKinley, Eliot; Wilson, David

    2006-03-01

    We developed a cryomicrotome/imaging system that provides high resolution, high sensitivity block-face images of whole mice or excised organs, and applied it to a variety of biological applications. With this cryo-imaging system, we sectioned cryo-preserved tissues at 2-40 μm thickness and acquired high resolution brightfield and fluorescence images with microscopic in-plane resolution (as good as 1.2 μm). Brightfield images of normal and pathological anatomy show exquisite detail, especially in the abdominal cavity. Multi-planar reformatting and 3D renderings allow one to interrogate 3D structures. In this report, we present brightfield images of mouse anatomy, as well as 3D renderings of organs. For BPK mice model of polycystic kidney disease, we compared brightfield cryo-images and kidney volumes to MRI. The color images provided greater contrast and resolution of cysts as compared to in vivo MRI. We note that color cryo-images are closer to what a researcher sees in dissection, making it easier for them to interpret image data. The combination of field of view, depth of field, ultra high resolution and color/fluorescence contrast enables cryo-image volumes to provide details that cannot be found through in vivo imaging or other ex vivo optical imaging approaches. We believe that this novel imaging system will have applications that include identification of mouse phenotypes, characterization of diseases like blood vessel disease, kidney disease, and cancer, assessment of drug and gene therapy delivery and efficacy and validation of other imaging modalities.

  4. Highly integrated image sensors enable low-cost imaging systems

    Science.gov (United States)

    Gallagher, Paul K.; Lake, Don; Chalmers, David; Hurwitz, J. E. D.

    1997-09-01

    The highest barriers to wide scale implementation of vision systems have been cost. This is closely followed by the level of difficulty of putting a complete imaging system together. As anyone who has every been in the position of creating a vision system knows, the various bits and pieces supplied by the many vendors are not under any type of standardization control. In short, unless you are an expert in imaging, electrical interfacing, computers, digital signal processing, and high speed storage techniques, you will likely spend more money trying to do it yourself rather than to buy the exceedingly expensive systems available. Another alternative is making headway into the imaging market however. The growing investment in highly integrated CMOS based imagers is addressing both the cost and the system integration difficulties. This paper discusses the benefits gained from CMOS based imaging, and how these benefits are already being applied.

  5. Tracing organizing principles: Learning from the history of systems biology

    DEFF Research Database (Denmark)

    Green, Sara; Wolkenhauer, Olaf

    2014-01-01

    on this historical background in order to increase the understanding of the motivation behind the search for general principles and to clarify different epistemic aims within systems biology. We pinpoint key aspects of earlier approaches that also underlie the current practice. These are i) the focus on relational......With the emergence of systems biology, the identification of organizing principles is being highlighted as a key research aim. Researchers attempt to “reverse engineer” the functional organization of biological systems using methodologies from mathematics, engineering and computer science while...... taking advantage of data produced by new experimental techniques. While systems biology is a relatively new approach, the quest for general principles of biological organization dates back to systems theoretic approaches in early and mid-twentieth century. The aim of this paper is to draw...

  6. Yeast systems biology to unravel the network of life

    DEFF Research Database (Denmark)

    Mustacchi, Roberta; Hohmann, S; Nielsen, Jens

    2006-01-01

    Systems biology focuses on obtaining a quantitative description of complete biological systems, even complete cellular function. In this way, it will be possible to perform computer-guided design of novel drugs, advanced therapies for treatment of complex diseases, and to perform in silico design....... Furthermore, it serves as an industrial workhorse for production of a wide range of chemicals and pharmaceuticals. Systems biology involves the combination of novel experimental techniques from different disciplines as well as functional genomics, bioinformatics and mathematical modelling, and hence no single...... laboratory has access to all the necessary competences. For this reason the Yeast Systems Biology Network (YSBN) has been established. YSBN will coordinate research efforts, in yeast systems biology and, through the recently obtained EU funding for a Coordination Action, it will be possible to set...

  7. Handheld microwave bomb-detecting imaging system

    Science.gov (United States)

    Gorwara, Ashok; Molchanov, Pavlo

    2017-05-01

    Proposed novel imaging technique will provide all weather high-resolution imaging and recognition capability for RF/Microwave signals with good penetration through highly scattered media: fog, snow, dust, smoke, even foliage, camouflage, walls and ground. Image resolution in proposed imaging system is not limited by diffraction and will be determined by processor and sampling frequency. Proposed imaging system can simultaneously cover wide field of view, detect multiple targets and can be multi-frequency, multi-function. Directional antennas in imaging system can be close positioned and installed in cell phone size handheld device, on small aircraft or distributed around protected border or object. Non-scanning monopulse system allows dramatically decrease in transmitting power and at the same time provides increased imaging range by integrating 2-3 orders more signals than regular scanning imaging systems.

  8. Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

    Science.gov (United States)

    Jalili, Mahdi

    2018-03-01

    I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

  9. Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

    NARCIS (Netherlands)

    He, F.; Murabito, E.; Westerhoff, H.V.

    2016-01-01

    Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

  10. Biological Detection System Technologies Technology and Industrial Base Study. A Primer on Biological Detection Technologies

    National Research Council Canada - National Science Library

    2001-01-01

    .... and Canadian military personnel. In light of these concerns both defense departments have increased efforts to develop and field biological agent detection systems to help protect their military forces and fixed assets...

  11. The Systems Biology Research Tool: evolvable open-source software

    Directory of Open Access Journals (Sweden)

    Wright Jeremiah

    2008-06-01

    Full Text Available Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology. Conclusion The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability, to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.

  12. Digital image display system for emergency room

    International Nuclear Information System (INIS)

    Murry, R.C.; Lane, T.J.; Miax, L.S.

    1989-01-01

    This paper reports on a digital image display system for the emergency room (ER) in a major trauma hospital. Its objective is to reduce radiographic image delivery time to a busy ER while simultaneously providing a multimodality capability. Image storage, retrieval, and display will also be facilitated with this system. The system's backbone is a token-ring network of RISC and personal computers. The display terminals are higher- function RISC computers with 1,024 2 color or gray-scale monitors. The PCs serve as administrative terminals. Nuclear medicine, CT, MR, and digitized film images are transferred to the image display system

  13. Technological Development of High-Performance MALDI Mass Spectrometry Imaging for the Study of Metabolic Biology

    Energy Technology Data Exchange (ETDEWEB)

    Feenstra, Adam D. [Iowa State Univ., Ames, IA (United States)

    2016-12-17

    This thesis represents efforts made in technological developments for the study of metabolic biology in plants, specifically maize, using matrix-assisted laser desorption/ ionization-mass spectrometry imaging.

  14. Scaling for Dynamical Systems in Biology.

    Science.gov (United States)

    Ledder, Glenn

    2017-11-01

    Asymptotic methods can greatly simplify the analysis of all but the simplest mathematical models and should therefore be commonplace in such biological areas as ecology and epidemiology. One essential difficulty that limits their use is that they can only be applied to a suitably scaled dimensionless version of the original dimensional model. Many books discuss nondimensionalization, but with little attention given to the problem of choosing the right scales and dimensionless parameters. In this paper, we illustrate the value of using asymptotics on a properly scaled dimensionless model, develop a set of guidelines that can be used to make good scaling choices, and offer advice for teaching these topics in differential equations or mathematical biology courses.

  15. Magnetic biosensor system to detect biological targets

    KAUST Repository

    Li, Fuquan

    2012-09-01

    Magneto-resistive sensors in combination with magnetic beads provide sensing platforms, which are small in size and highly sensitive. These platforms can be fully integrated with microchannels and electronics to enable devices capable of performing complex tasks. Commonly, a sandwich method is used that requires a specific coating of the sensor\\'s surface to immobilize magnetic beads and biological targets on top of the sensor. This paper concerns a micro device to detect biological targets using magnetic concentration, magnetic as well as mechanical trapping and magnetic sensing. Target detection is based on the size difference between bare magnetic beads and magnetic beads with targets attached. This method remedies the need for a coating layer and reduces the number of steps required to run an experiment. © 2012 IEEE.

  16. A fractal-based image encryption system

    KAUST Repository

    Abd-El-Hafiz, S. K.; Radwan, Ahmed Gomaa; Abdel Haleem, Sherif H.; Barakat, Mohamed L.

    2014-01-01

    single-fractal image and statistical analysis is performed. A general encryption system utilising multiple fractal images is, then, introduced to improve the performance and increase the encryption key up to hundreds of bits. This improvement is achieved

  17. Synthetic Biology: Engineering Living Systems from Biophysical Principles.

    Science.gov (United States)

    Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

    2017-03-28

    Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  18. Principles of Systems Biology, No. 29.

    Science.gov (United States)

    2018-05-23

    This month: in silico labeling of microscopy images (Christiansen/Finkbeiner), single-cell lineage trees and data integration (Rajewsky, Satija), gene expression (Weinberger/Simpson, Tavazoie, Ameres/Zuber), and signalling networks (Mercer/Wollscheid, Fussenegger). Copyright © 2018. Published by Elsevier Inc.

  19. Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution

    Science.gov (United States)

    Joens, Matthew S.; Huynh, Chuong; Kasuboski, James M.; Ferranti, David; Sigal, Yury J.; Zeitvogel, Fabian; Obst, Martin; Burkhardt, Claus J.; Curran, Kevin P.; Chalasani, Sreekanth H.; Stern, Lewis A.; Goetze, Bernhard; Fitzpatrick, James A. J.

    2013-12-01

    Scanning Electron Microscopy (SEM) has long been the standard in imaging the sub-micrometer surface ultrastructure of both hard and soft materials. In the case of biological samples, it has provided great insights into their physical architecture. However, three of the fundamental challenges in the SEM imaging of soft materials are that of limited imaging resolution at high magnification, charging caused by the insulating properties of most biological samples and the loss of subtle surface features by heavy metal coating. These challenges have recently been overcome with the development of the Helium Ion Microscope (HIM), which boasts advances in charge reduction, minimized sample damage, high surface contrast without the need for metal coating, increased depth of field, and 5 angstrom imaging resolution. We demonstrate the advantages of HIM for imaging biological surfaces as well as compare and contrast the effects of sample preparation techniques and their consequences on sub-nanometer ultrastructure.

  20. Programmed Multi-Image Lectures for College Biology Instruction.

    Science.gov (United States)

    Jensen, William A.; Knauft, Robert L.

    1977-01-01

    Discusses the use of a programed multi-image lecture approach for teaching a botany course to nonmajor students at the University of California, Berkeley. Also considers the advantages, production, method of presentation, and design of the multimedia lectures. (HM)

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

    Science.gov (United States)

    Chandra, Subhash

    2008-12-01

    provided a rule-of-thumb criterion for the validation of sample preparation. The fractured freeze-dried cells allowed 3-D SIMS imaging and localization of 13C 15N labeled molecules and therapeutic drugs containing an elemental tag. Examples are shown to demonstrate that both diffusible elements and molecules are prone to artifact-induced relocation at subcellular scale if the sample preparation is compromised. The sample preparation is problem dependent and may vary widely between the diverse sample types of biological systems and the type of instrument used for SIMS analysis. The sample preparation, however, must be validated so that SIMS can be applied with confidence in biology and medicine.

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

    International Nuclear Information System (INIS)

    Chandra, Subhash

    2008-01-01

    provided a rule-of-thumb criterion for the validation of sample preparation. The fractured freeze-dried cells allowed 3-D SIMS imaging and localization of 13 C 15 N labeled molecules and therapeutic drugs containing an elemental tag. Examples are shown to demonstrate that both diffusible elements and molecules are prone to artifact-induced relocation at subcellular scale if the sample preparation is compromised. The sample preparation is problem dependent and may vary widely between the diverse sample types of biological systems and the type of instrument used for SIMS analysis. The sample preparation, however, must be validated so that SIMS can be applied with confidence in biology and medicine

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

    Directory of Open Access Journals (Sweden)

    Yoshihiro Kawano

    Full Text Available 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.

  4. Objective analysis of image quality of video image capture systems

    Science.gov (United States)

    Rowberg, Alan H.

    1990-07-01

    As Picture Archiving and Communication System (PACS) technology has matured, video image capture has become a common way of capturing digital images from many modalities. While digital interfaces, such as those which use the ACR/NEMA standard, will become more common in the future, and are preferred because of the accuracy of image transfer, video image capture will be the dominant method in the short term, and may continue to be used for some time because of the low cost and high speed often associated with such devices. Currently, virtually all installed systems use methods of digitizing the video signal that is produced for display on the scanner viewing console itself. A series of digital test images have been developed for display on either a GE CT9800 or a GE Signa MRI scanner. These images have been captured with each of five commercially available image capture systems, and the resultant images digitally transferred on floppy disk to a PC1286 computer containing Optimast' image analysis software. Here the images can be displayed in a comparative manner for visual evaluation, in addition to being analyzed statistically. Each of the images have been designed to support certain tests, including noise, accuracy, linearity, gray scale range, stability, slew rate, and pixel alignment. These image capture systems vary widely in these characteristics, in addition to the presence or absence of other artifacts, such as shading and moire pattern. Other accessories such as video distribution amplifiers and noise filters can also add or modify artifacts seen in the captured images, often giving unusual results. Each image is described, together with the tests which were performed using them. One image contains alternating black and white lines, each one pixel wide, after equilibration strips ten pixels wide. While some systems have a slew rate fast enough to track this correctly, others blur it to an average shade of gray, and do not resolve the lines, or give

  5. Characterization of lens based photoacoustic imaging system

    Directory of Open Access Journals (Sweden)

    Kalloor Joseph Francis

    2017-12-01

    Full Text Available Some of the challenges in translating photoacoustic (PA imaging to clinical applications includes limited view of the target tissue, low signal to noise ratio and the high cost of developing real-time systems. Acoustic lens based PA imaging systems, also known as PA cameras are a potential alternative to conventional imaging systems in these scenarios. The 3D focusing action of lens enables real-time C-scan imaging with a 2D transducer array. In this paper, we model the underlying physics in a PA camera in the mathematical framework of an imaging system and derive a closed form expression for the point spread function (PSF. Experimental verification follows including the details on how to design and fabricate the lens inexpensively. The system PSF is evaluated over a 3D volume that can be imaged by this PA camera. Its utility is demonstrated by imaging phantom and an ex vivo human prostate tissue sample.

  6. Characterization of lens based photoacoustic imaging system.

    Science.gov (United States)

    Francis, Kalloor Joseph; Chinni, Bhargava; Channappayya, Sumohana S; Pachamuthu, Rajalakshmi; Dogra, Vikram S; Rao, Navalgund

    2017-12-01

    Some of the challenges in translating photoacoustic (PA) imaging to clinical applications includes limited view of the target tissue, low signal to noise ratio and the high cost of developing real-time systems. Acoustic lens based PA imaging systems, also known as PA cameras are a potential alternative to conventional imaging systems in these scenarios. The 3D focusing action of lens enables real-time C-scan imaging with a 2D transducer array. In this paper, we model the underlying physics in a PA camera in the mathematical framework of an imaging system and derive a closed form expression for the point spread function (PSF). Experimental verification follows including the details on how to design and fabricate the lens inexpensively. The system PSF is evaluated over a 3D volume that can be imaged by this PA camera. Its utility is demonstrated by imaging phantom and an ex vivo human prostate tissue sample.

  7. Analysis of image plane's Illumination in Image-forming System

    International Nuclear Information System (INIS)

    Duan Lihua; Zeng Yan'an; Zhang Nanyangsheng; Wang Zhiguo; Yin Shiliang

    2011-01-01

    In the detection of optical radiation, the detecting accuracy is affected by optic power distribution of the detector's surface to a large extent. In addition, in the image-forming system, the quality of the image is greatly determined by the uniformity of the image's illumination distribution. However, in the practical optical system, affected by the factors such as field of view, false light and off axis and so on, the distribution of the image's illumination tends to be non uniform, so it is necessary to discuss the image plane's illumination in image-forming systems. In order to analyze the characteristics of the image-forming system at a full range, on the basis of photometry, the formulas to calculate the illumination of the imaging plane have been summarized by the numbers. Moreover, the relationship between the horizontal offset of the light source and the illumination of the image has been discussed in detail. After that, the influence of some key factors such as aperture angle, off-axis distance and horizontal offset on illumination of the image has been brought forward. Through numerical simulation, various theoretical curves of those key factors have been given. The results of the numerical simulation show that it is recommended to aggrandize the diameter of the exit pupil to increase the illumination of the image. The angle of view plays a negative role in the illumination distribution of the image, that is, the uniformity of the illumination distribution can be enhanced by compressing the angle of view. Lastly, it is proved that telecentric optical design is an effective way to advance the uniformity of the illumination distribution.

  8. Fluoroscopic Imaging Systems. Chapter 8

    Energy Technology Data Exchange (ETDEWEB)

    Jones, A. K. [University of Texas MD Anderson Cancer Center, Houston (United States)

    2014-09-15

    Fluoroscopy refers to the use of an X ray beam and a suitable image receptor for viewing images of processes or instruments in the body in real time. Fluoroscopic imaging trades the high signal to noise ratio (SNR) of radiography for high temporal resolution, as factors that maintain patient dose at an acceptable level must be used.

  9. Behaviors of tritium in terrestrial biological system

    International Nuclear Information System (INIS)

    Inomata, Tsuyako

    1983-01-01

    The in vivo behaviors of HTO- 3 H in food chain models in experimental animals were described. Of pregnant mice that had ingested HTO and drinking water alone for 19 days, the total 3 H content in the tissue/wet weight was greater by 20% in fetuses and newborns than in mothers, and the proportion of tissue-bound 3 H was 8-24% in mothers and 3% in fetuses. The mean 3 H concentration in the free water in tissues was about 36% of ingested HTO. When only 3 H foods were ingested for 18 days, the total 3 H content in the tissue/wet weight showed no marked difference among the mother, fetuses and newborns, nor did the bound 3 H level show great differences. With respect to the tissue distribution of 3 H, only the incorporation rate by the mother's brain from HTO was satisfactory, whereas in other organs, the mother, fetuses and newborns showed higher incorporation rates from 3 H foods. The ratio of specific radioactivity of soft tissue 3 H in mothers to HTO in drinking water exceeded 1 only for the spleen, but other tissues showed no biological concentration. Again, no biological concentration was observed with 3 H foods. Environmental HTO did not result in biological concentration of 3 H in mother mice that had ingested 3 H foods, but 3 H was rather diluted. Tissues other than the spleen showed similar values of 3 H ingestion from environmental HTO through all routes. However, the proportion of bound 3 H in the total 3 H in the soft tissue was about 1.4-1.6 times that on ingestion of HTO alone. (Chiba, N.)

  10. Optical Biosensors to Explore Biological Systems

    DEFF Research Database (Denmark)

    Palanco, Marta Espina; Mogensen, Klaus Bo; Andersen, Nils H. Skovgaard

    2016-01-01

    their capability to work in biosensor devices. For example, Raman spectroscopy can be non-invasive and can provide 1 μm of spatial resolution in 1 second of collection time, well suited for sensing. Moreover, it may give information at the single cell and even approaching the single molecule scale. Here we present...... protein may be used as an efficient sensor in an organic environment via a biomimetic membrane model. The combination of both biomimetic membranes and protein membranes as a signal transduction medium has interesting applications in biology and medicine. It is crucial that the matrix where a protein...

  11. PET imaging for the quantification of biologically heterogeneous tumours: measuring the effect of relative position on image-based quantification of dose-painting targets

    International Nuclear Information System (INIS)

    McCall, Keisha C; Barbee, David L; Kissick, Michael W; Jeraj, Robert

    2010-01-01

    Quantitative imaging of tumours represents the foundation of customized therapies and adaptive patient care. As such, we have investigated the effect of patient positioning errors on the reproducibility of images of biologically heterogeneous tumours generated by a clinical PET/CT system. A commercial multi-slice PET/CT system was used to acquire 2D and 3D PET images of a phantom containing multiple spheres of known volumes and known radioactivity concentrations and suspended in an aqueous medium. The spheres served as surrogates for sub-tumour regions of biological heterogeneities with dimensions of 5-15 mm. Between image acquisitions, a motorized-arm was used to reposition the spheres in 1 mm intervals along either the radial or the axial direction. Images of the phantom were reconstructed using typical diagnostic reconstruction techniques, and these images were analysed to characterize and model the position-dependent changes in contrast recovery. A simulation study was also conducted to investigate the effect of patient position on the reproducibility of PET imaging of biologically heterogeneous head and neck (HN) tumours. For this simulation study, we calculated the changes in image intensity values that would occur with changes in the relative position of the patients at the time of imaging. PET images of two HN patients were used to simulate an imaging study that incorporated set-up errors that are typical for HN patients. One thousand randomized positioning errors were investigated for each patient. As a result of the phantom study, a position-dependent trend was identified for measurements of contrast recovery of small objects. The peak contrast recovery occurred at radial and axial positions that coincide with the centre of the image voxel. Conversely, the minimum contrast recovery occurred when the object was positioned at the edges of the image voxel. Changing the position of high contrast spheres by one-half the voxel dimension lead to errors in the

  12. Developing stereo image based robot control system

    Energy Technology Data Exchange (ETDEWEB)

    Suprijadi,; Pambudi, I. R.; Woran, M.; Naa, C. F; Srigutomo, W. [Department of Physics, FMIPA, InstitutTeknologi Bandung Jl. Ganesha No. 10. Bandung 40132, Indonesia supri@fi.itb.ac.id (Indonesia)

    2015-04-16

    Application of image processing is developed in various field and purposes. In the last decade, image based system increase rapidly with the increasing of hardware and microprocessor performance. Many fields of science and technology were used this methods especially in medicine and instrumentation. New technique on stereovision to give a 3-dimension image or movie is very interesting, but not many applications in control system. Stereo image has pixel disparity information that is not existed in single image. In this research, we proposed a new method in wheel robot control system using stereovision. The result shows robot automatically moves based on stereovision captures.

  13. Noninvasive biological sensor system for detection of drunk driving.

    Science.gov (United States)

    Murata, Kohji; Fujita, Etsunori; Kojima, Shigeyuki; Maeda, Shinitirou; Ogura, Yumi; Kamei, Tsutomu; Tsuji, Toshio; Kaneko, Shigehiko; Yoshizumi, Masao; Suzuki, Nobutaka

    2011-01-01

    Systems capable of monitoring the biological condition of a driver and issuing warnings during instances of drowsiness have recently been studied. Moreover, many researchers have reported that biological signals, such as brain waves, pulsation waves, and heart rate, are different between people who have and have not consumed alcohol. Currently, we are developing a noninvasive system to detect individuals driving under the influence of alcohol by measuring biological signals. We used the frequency time series analysis to attempt to distinguish between normal and intoxicated states of a person as the basis of the sensing system.

  14. Biochemical Space: A Framework for Systemic Annotation of Biological Models

    Czech Academy of Sciences Publication Activity Database

    Klement, M.; Děd, T.; Šafránek, D.; Červený, Jan; Müller, Stefan; Steuer, Ralf

    2014-01-01

    Roč. 306, JUL (2014), s. 31-44 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * cyanobacteria Subject RIV: EH - Ecology, Behaviour

  15. Review of "Stochastic Modelling for Systems Biology" by Darren Wilkinson

    Directory of Open Access Journals (Sweden)

    Bullinger Eric

    2006-12-01

    Full Text Available Abstract "Stochastic Modelling for Systems Biology" by Darren Wilkinson introduces the peculiarities of stochastic modelling in biology. This book is particularly suited to as a textbook or for self-study, and for readers with a theoretical background.

  16. A systems biology approach to study systemic inflammation.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2014-01-01

    Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

  17. BIOCAT: a pattern recognition platform for customizable biological image classification and annotation.

    Science.gov (United States)

    Zhou, Jie; Lamichhane, Santosh; Sterne, Gabriella; Ye, Bing; Peng, Hanchuan

    2013-10-04

    Pattern recognition algorithms are useful in bioimage informatics applications such as quantifying cellular and subcellular objects, annotating gene expressions, and classifying phenotypes. To provide effective and efficient image classification and annotation for the ever-increasing microscopic images, it is desirable to have tools that can combine and compare various algorithms, and build customizable solution for different biological problems. However, current tools often offer a limited solution in generating user-friendly and extensible tools for annotating higher dimensional images that correspond to multiple complicated categories. We develop the BIOimage Classification and Annotation Tool (BIOCAT). It is able to apply pattern recognition algorithms to two- and three-dimensional biological image sets as well as regions of interest (ROIs) in individual images for automatic classification and annotation. We also propose a 3D anisotropic wavelet feature extractor for extracting textural features from 3D images with xy-z resolution disparity. The extractor is one of the about 20 built-in algorithms of feature extractors, selectors and classifiers in BIOCAT. The algorithms are modularized so that they can be "chained" in a customizable way to form adaptive solution for various problems, and the plugin-based extensibility gives the tool an open architecture to incorporate future algorithms. We have applied BIOCAT to classification and annotation of images and ROIs of different properties with applications in cell biology and neuroscience. BIOCAT provides a user-friendly, portable platform for pattern recognition based biological image classification of two- and three- dimensional images and ROIs. We show, via diverse case studies, that different algorithms and their combinations have different suitability for various problems. The customizability of BIOCAT is thus expected to be useful for providing effective and efficient solutions for a variety of biological

  18. Transfer function analysis of radiographic imaging systems

    International Nuclear Information System (INIS)

    Metz, C.E.; Doi, K.

    1979-01-01

    The theoretical and experimental aspects of the techniques of transfer function analysis used in radiographic imaging systems are reviewed. The mathematical principles of transfer function analysis are developed for linear, shift-invariant imaging systems, for the relation between object and image and for the image due to a sinusoidal plane wave object. The other basic mathematical principle discussed is 'Fourier analysis' and its application to an input function. Other aspects of transfer function analysis included are alternative expressions for the 'optical transfer function' of imaging systems and expressions are derived for both serial and parallel transfer image sub-systems. The applications of transfer function analysis to radiographic imaging systems are discussed in relation to the linearisation of the radiographic imaging system, the object, the geometrical unsharpness, the screen-film system unsharpness, other unsharpness effects and finally noise analysis. It is concluded that extensive theoretical, computer simulation and experimental studies have demonstrated that the techniques of transfer function analysis provide an accurate and reliable means for predicting and understanding the effects of various radiographic imaging system components in most practical diagnostic medical imaging situations. (U.K.)

  19. 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.

  20. 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.

  1. Multispectral system for medical fluorescence imaging

    International Nuclear Information System (INIS)

    Andersson, P.S.; Montan, S.; Svanberg, S.

    1987-01-01

    The principles of a powerful multicolor imaging system for tissue fluorescence diagnostics are discussed. Four individually spectrally filtered images are formed on a matrix detector by means of a split-mirror arrangement. The four images are processed in a computer, pixel by pixel, by means of mathematical operations, leading to an optimized contrast image, which enhances a selected feature. The system is being developed primarily for medical fluorescence imaging, but has wide applications in fluorescence, reflectance, and transmission monitoring related to a wide range of industrial and environmental problems. The system operation is described for the case of linear imaging on a diode array detector. Laser-induced fluorescence is used for cancer tumor and arteriosclerotic plaque demarcation using the contrast enhancement capabilities of this imaging system. Further examples of applications include fluorescing minerals and flames

  2. A high brightness probe of polymer nanoparticles for biological imaging

    Science.gov (United States)

    Zhou, Sirong; Zhu, Jiarong; Li, Yaping; Feng, Liheng

    2018-03-01

    Conjugated polymer nanoparticles (CPNs) with high brightness in long wavelength region were prepared by the nano-precipitation method. Based on fluorescence resonance energy transfer (FRET) mechanism, the high brightness property of the CPNs was realized by four different emission polymers. Dynamic light scattering (DLS) and scanning electron microscopy (SEM) displayed that the CPNs possessed a spherical structure and an average diameter of 75 nm. Analysis assays showed that the CPNs had excellent biocompatibility, good photostability and low cytotoxicity. The CPNs were bio-modified with a cell penetrating peptide (Tat, a targeted element) through covalent link. Based on the entire wave fluorescence emission, the functionalized CPNs1-4 can meet multichannel and high throughput assays in cell and organ imaging. The contribution of the work lies in not only providing a new way to obtain a high brightness imaging probe in long wavelength region, but also using targeted cell and organ imaging.

  3. Multi-level and hybrid modelling approaches for systems biology.

    Science.gov (United States)

    Bardini, R; Politano, G; Benso, A; Di Carlo, S

    2017-01-01

    During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

  4. Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

    Science.gov (United States)

    Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

    2015-08-21

    In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

  5. 3D images and expert system

    International Nuclear Information System (INIS)

    Hasegawa, Jun-ichi

    1998-01-01

    This paper presents an expert system called 3D-IMPRESS for supporting applications of three dimensional (3D) image processing. This system can automatically construct a 3D image processing procedure based on a pictorial example of the goal given by a user. In the paper, to evaluate the performance of the system, it was applied to construction of procedures for extracting specific component figures from practical chest X-ray CT images. (author)

  6. 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.

  7. A universal fluid cell for the imaging of biological specimens in the atomic force microscope.

    Science.gov (United States)

    Kasas, Sandor; Radotic, Ksenja; Longo, Giovanni; Saha, Bashkar; Alonso-Sarduy, Livan; Dietler, Giovanni; Roduit, Charles

    2013-04-01

    Recently, atomic force microscope (AFM) manufacturers have begun producing instruments specifically designed to image biological specimens. In most instances, they are integrated with an inverted optical microscope, which permits concurrent optical and AFM imaging. An important component of the set-up is the imaging chamber, whose design determines the nature of the experiments that can be conducted. Many different imaging chamber designs are available, usually designed to optimize a single parameter, such as the dimensions of the substrate or the volume of fluid that can be used throughout the experiment. In this report, we present a universal fluid cell, which simultaneously optimizes all of the parameters that are important for the imaging of biological specimens in the AFM. This novel imaging chamber has been successfully tested using mammalian, plant, and microbial cells. Copyright © 2013 Wiley Periodicals, Inc.

  8. Sensitivity analysis approaches applied to systems biology models.

    Science.gov (United States)

    Zi, Z

    2011-11-01

    With the rising application of systems biology, sensitivity analysis methods have been widely applied to study the biological systems, including metabolic networks, signalling pathways and genetic circuits. Sensitivity analysis can provide valuable insights about how robust the biological responses are with respect to the changes of biological parameters and which model inputs are the key factors that affect the model outputs. In addition, sensitivity analysis is valuable for guiding experimental analysis, model reduction and parameter estimation. Local and global sensitivity analysis approaches are the two types of sensitivity analysis that are commonly applied in systems biology. Local sensitivity analysis is a classic method that studies the impact of small perturbations on the model outputs. On the other hand, global sensitivity analysis approaches have been applied to understand how the model outputs are affected by large variations of the model input parameters. In this review, the author introduces the basic concepts of sensitivity analysis approaches applied to systems biology models. Moreover, the author discusses the advantages and disadvantages of different sensitivity analysis methods, how to choose a proper sensitivity analysis approach, the available sensitivity analysis tools for systems biology models and the caveats in the interpretation of sensitivity analysis results.

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

    Science.gov (United States)

    Kimori, Yoshitaka; Baba, Norio; Morone, Nobuhiro

    2010-07-08

    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. 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. 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.

  10. A system for success: BMC Systems Biology, a new open access journal

    OpenAIRE

    Webb Penelope A; Hodgkinson Matt J

    2007-01-01

    Abstract BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  11. A system for success: BMC Systems Biology, a new open access journal.

    Science.gov (United States)

    Hodgkinson, Matt J; Webb, Penelope A

    2007-09-04

    BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

  12. 'TISUCROMA': A Software for Color Processing of Biological Tissue's Images

    International Nuclear Information System (INIS)

    Arista Romeu, Eduardo J.; La Rosa Vazquez, Jose Manuel de; Valor, Alma; Stolik, Suren

    2016-01-01

    In this work a software intended to plot and analyze digital image RGB histograms from normal and abnormal regions of biological tissue. The obtained RGB histograms from each zone can be used to show the image in only one color or the mixture of some of them. The Software was developed in Lab View to process the images in a laptop. Some medical application examples are shown. (Author)

  13. Systems biology of neutrophil differentiation and immune response

    DEFF Research Database (Denmark)

    Theilgaard-Mönch, Kim; Porse, Bo T; Borregaard, Niels

    2005-01-01

    Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies. These stu......Systems biology has emerged as a new scientific field, which aims at investigating biological processes at the genomic and proteomic levels. Recent studies have unravelled aspects of neutrophil differentiation and immune responses at the systems level using high-throughput technologies....... These studies have identified a plethora of novel effector proteins stored in the granules of neutrophils. In addition, these studies provide evidence that neutrophil differentiation and immune response are governed by a highly coordinated transcriptional programme that regulates cellular fate and function...

  14. Advancing metabolic engineering through systems biology of industrial microorganisms.

    Science.gov (United States)

    Dai, Zongjie; Nielsen, Jens

    2015-12-01

    Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Advancing metabolic engineering through systems biology of industrial microorganisms

    DEFF Research Database (Denmark)

    Dai, Zongjie; Nielsen, Jens

    2015-01-01

    resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review......Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

  16. Systems biology approaches to the study of cardiovascular drugs

    NARCIS (Netherlands)

    Nikolsky, Y.; Kleemann, R.

    2010-01-01

    Atherogenic lipids and chronic inflammation drive the development of cardiovascular disorders such as atherosclerosis. Many cardiovascular drugs target the liver which is involved in the formation of lipid and inflammatory risk factors. With robust systems biology tools and comprehensive

  17. Strategies for structuring interdisciplinary education in Systems Biology

    DEFF Research Database (Denmark)

    Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure

    2016-01-01

    function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material...... and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active...... performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii...

  18. Flow imaging of the cardiovascular system using magnetic resonance imaging

    International Nuclear Information System (INIS)

    Imai, Hitoshi; Sakakibara, Makoto; Sunami, Yuko

    1988-01-01

    Blood flow images by magnetic resonance imaging (MRI) using a 0.25 T unit were evaluated for nine normal volunteers and 108 subjects with a variety of cardiovascular abnormalities. Using the non-gated short-spin echo (SE) technique, blood flow in the cardiovascular systems was not imaged in the normal volunteers. Using end-systolic and end-diastolic SE techniques for the normal subjects, blood flow in the cardiac chambers was not clearly imaged. Blood flow in the ascending aorta and aortic arch often did not appear in the gated SE images of the normal subjects. However, blood flow in the descending aorta was often observed in the gated SE images. Blood flow imaging was demonstrated by both non-gated and gated SE techniques in regions where blood flow was relatively slow; for example, in the left atrium of mitral stenosis, in an aortic aneurysm, in a false lumen of an aortic dissection, and in the left ventricle having old myocardial infarction. Using the non-gated inversion recovery (IR) technique, no blood flow was imaged in the cardiovascular system except in the left atrium of one case with mitral stenosis. Using the non-gated short SE technique, there was good correlation between the thrombus formation and the presence of blood flow images in the left atria of 17 patients with mitral stenosis, and in the aneurysmal portions of the aorta or in the false lumens of aortic dissection of 18 patients. It was suggested that mural thrombi in such diseases were related to the relatively slow blood flow. Blood flow imaging easily distinguished stagnant blood flow from mural thrombi using non-gated short SE, end-systolic SE, and IR techniques. Thus, blood flow imaging using MRI should become an important means of evaluating the cardiovascular system. (author)

  19. 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.

  20. Dynamic MR imaging of the musculoskeletal system

    International Nuclear Information System (INIS)

    Shah, A.S.; Hylton, H.; Hentz, V.R.; Schattner, P.

    1991-01-01

    This paper reports on dynamic MR imaging which is an MR technique that allows imaging of the musculoskeletal system in motion. Current methods for observing the articulation of muscles and joints are limited to acquisition of stationary images at different spatial orientations. These images are then replayed from computer memory to simulate motion. Unlike stationary acquisition, dynamic MR imaging allows the volume of interest to be subjected to motion and dynamic stress, which is important for detecting stress-induced pathology. To demonstrate the utility of dynamic MR imaging, a system for imaging a moving wrist has been developed. The system consists of apparatus capable of providing simultaneous radialulnar deviation and flexion-extension, and hardware for system control and acquisition gating. The apparatus is mounted on the patient bed and is transferable to a variety of standard clinical MR imaging systems. Images were obtained during motion, and the ability of dynamic MR imaging to accurately image the moving wrist with very little motion artifact was demonstrated

  1. Image processing of integrated video image obtained with a charged-particle imaging video monitor system

    International Nuclear Information System (INIS)

    Iida, Takao; Nakajima, Takehiro

    1988-01-01

    A new type of charged-particle imaging video monitor system was constructed for video imaging of the distributions of alpha-emitting and low-energy beta-emitting nuclides. The system can display not only the scintillation image due to radiation on the video monitor but also the integrated video image becoming gradually clearer on another video monitor. The distortion of the image is about 5% and the spatial resolution is about 2 line pairs (lp)mm -1 . The integrated image is transferred to a personal computer and image processing is performed qualitatively and quantitatively. (author)

  2. Category of Metabolic-Replication Systems in Biology and Medicine

    OpenAIRE

    I. C. Baianu

    2012-01-01

    Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life's origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important questio...

  3. Exploring Synthetic and Systems Biology at the University of Edinburgh.

    Science.gov (United States)

    Fletcher, Liz; Rosser, Susan; Elfick, Alistair

    2016-06-15

    The Centre for Synthetic and Systems Biology ('SynthSys') was originally established in 2007 as the Centre for Integrative Systems Biology, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC). Today, SynthSys embraces an extensive multidisciplinary community of more than 200 researchers from across the University with a common interest in synthetic and systems biology. Our research is broad and deep, addressing a diversity of scientific questions, with wide ranging impact. We bring together the power of synthetic biology and systems approaches to focus on three core thematic areas: industrial biotechnology, agriculture and the environment, and medicine and healthcare. In October 2015, we opened a newly refurbished building as a physical hub for our new U.K. Centre for Mammalian Synthetic Biology funded by the BBSRC/EPSRC/MRC as part of the U.K. Research Councils' Synthetic Biology for Growth programme. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  4. Fast removal of oxygen from biological systems

    International Nuclear Information System (INIS)

    Dewey, D.L.; Michael, B.D.

    1975-01-01

    Reference is made to the fact that if radiation is given at a high enough dose rate, the biological effect of oxygen is less than at low dose rates. Examples are given of 'break-point' experiments showing the effect. It is stated that the rapid removal of a substance by radiation is not confined to oxygen: the only criterion required to demonstrate the effect is that the chemical causes a measurable sensitization or protection at a concentration small enough so that it can be depleted at a relatively low dose of radiation. Sufficient confidence is now placed in the effect that it can be used the other way round; that is, to measure the position of the break-point and from this measurement determine the oxygen concentration at the target site at the instant before irradiation. Examples are given of the use of the high dose rate technique for measuring the oxygen concentration inside mammalian cells (Chinese hamster cells). The effects of partial pressures of inert gases, and the effect of elevated gas pressures, are discussed. (U.K.)

  5. Primary energy-transformations in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Lehninger, A.L.

    1980-10-01

    In this paper I shall review the main outlines of current research on the molecular aspects of the primary energy-coupling mechanisms in cells, those carried out by energy-transducing membranes. They include the capture of solar energy by the chloroplast membranes of green plants, used to generate carbohydrates and molecular oxygen from carbon dioxide and water, and the counterpart of photosynthesis, the process of respiration in heterotrophic organisms, in which reduced organic products generated by photosynthesis are oxidized at the expense of dioxygen to form carbon dioxide and water. Although the cycling of dioxygen, carbon dioxide, and organic matter between the plant and animal worlds is well known, it is not generally appreciated that the magnitude of biological energy flux in these cycles is huge compared to the total energy flux in man-made devices. A major consequence is that the concentration of carbon dioxide in the atmosphere has been increasing at a significant rate, at a time when there is also a decrease, at least in some parts of the world, in the counterbalancing utilization of CO/sub 2/ by green plants, due to deforestation. The greenhouse effect of increased atmospheric CO/sub 2/ may not only change the earth's climate, but also may influence the rate of photosynthesis. It is also not generally appreciated that energy flow in the biosphere leads to production of enormous amounts of organic matter potentially useful in furnishing man's energy requirements.

  6. System chemical biology studies of endocrine disruptors

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Oprea, Tudor I.

    Endocrine disrupting chemicals (EDCs) alter hormonal balance and other physiological systems through inappropriate developmental or adult exposure, perturbing the reproductive function of further generations. While disruption of key receptors (e.g., estrogen, androgen, and thyroid) at the ligand...

  7. Hydroxyapatite crystal deposition disease: imaging aspects and biological behavior

    International Nuclear Information System (INIS)

    D'Aquino, Danilo Olavarria; Pinto, Alexandre de Lavra; Costa, Mauro Jose Brandao da; Fanelli, Vania A.; Abud, Lucas Giansante

    2005-01-01

    Objective: to demonstrate, using imaging methods (x-ray, computed tomography (CT), magnetic resonance imaging (MRI) and ultrasound (US), the phases of hydroxyapatite crystal deposition disease in joints, particularly in the shoulder, from the silent phase to the intra-osseous migration of calcifications and radiologic follow-up examinations showing complete remission after physical therapy. Material and method: we evaluated 27 joints (25 shoulders, one hip and one elbow) of patients followed-up with radiographs. Patients extremely symptomatic and refractory to treatment were referred to MRI or US. Results: total remission of calcifications was observed in 15 joints after treatment - 14 shoulders and one elbow. In two joint, migration of the calcification to bone was observed: one to the bursa subdeltoidea, one to biceps tendon, one to subcoracoid recess and one to the interior of the infra spinal muscle. In two cases MRI and CT scans showed a high inflammatory process triggered by the disease. Conclusion: hydroxyapatite crystal deposition disease affects multiple joints and can vary from asymptomatic to extremely symptomatic. Imaging methods show all phases of the disease, including the migratory phase. In general, the use of x-ray is enough for the diagnosis and follow-up. MRI and CT provide a more accurate diagnosis in the active phase of the disease. In this paper, remission was seen with physiotherapy (iontophoresis) in 55% of the cases. (author)

  8. The application of near-infrared spectra micro-image in the imaging analysis of biology samples

    Directory of Open Access Journals (Sweden)

    Dong Wang

    2014-07-01

    Full Text Available In this research, suitable imaging methods were used for acquiring single compound images of biology samples of chicken pectorales tissue section, tobacco dry leaf, fresh leaf and plant glandular hair, respectively. The adverse effects caused by the high water content and the thermal effect of near infrared (NIR light were effectively solved during the experiment procedures and the data processing. PCA algorithm was applied to the NIR micro-image of chicken pectorales tissue. Comparing the loading vector of PC3 with the NIR spectrum of dry albumen, the information of PC3 was confirmed to be provided mainly by protein, i.e., the 3rd score image represents the distribution trend of protein mainly. PCA algorithm was applied to the NIR micro-image of tobacco dry leaf. The information of PC2 was confirmed to be provided by carbohydrate including starch mainly. Compared to the 2nd score image of tobacco dry leaf, the compared correlation image with the reference spectrum of starch had the same distribution trend as the 2nd score image. The comparative correlation images with the reference spectra of protein, glucose, fructose and the total plant alkaloid were acquired to confirm the distribution trend of these compounds in tobacco dry leaf respectively. Comparative correlation images of fresh leaf with the reference spectra of protein, starch, fructose, glucose and water were acquired to confirm the distribution trend of these compounds in fresh leaf. Chemimap imaging of plant glandular hair was acquired to show the tubular structure clearly.

  9. A Generic Language for Biological Systems based on Bigraphs

    DEFF Research Database (Denmark)

    Damgaard, Troels Christoffer; Krivine, Jean

    Several efforts have shown that process calculi developed for reasoning about concurrent and mobile systems may be employed for modelling biological systems at the molecular level. In this paper, we initiate investigation of the meta-language framework bigraphical reactive systems, due to Milner et...

  10. Digital image information systems in radiology

    International Nuclear Information System (INIS)

    Greinacher, C.F.C.; Luetke, B.; Seufert, G.

    1987-01-01

    About 25% of all patient examinations are performed digitally in a today's radiological department. A computerized system is described that supports generation, transport, interpretation and archiving of digital radiological images (Picture Archiving and Communication System PACS). The technical features concerning image communication via local area networks, image storage on magnetic and optical media and digital workstations for image display and manipulation are described. A structured system architecture is introduced. It allows flexible adaption to individual organizations and minimizes the requirements of the communication network. (orig.) [de

  11. Biocellion: accelerating computer simulation of multicellular biological system models.

    Science.gov (United States)

    Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

    2014-11-01

    Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Biological oceanography of the red oceanic system

    Science.gov (United States)

    Theil, Hjalmar; Weikert, Horst

    1. In 1977, 1979 and 1980-81, investigations were carried out which aimed at evaluating the potential risks from mining metalliferous muds precipating in the Atlantis II Deep of the central Red Sea. This environmental research was initiated by the Saudi Sudanese Red Sea Joint Commission in order to avoid any danger for the Red Sea ecosystem. The broad environmental research programme coherent studies in physical, chemical, biological, and geological oceanography as well as toxicological investigations in the oceanic and in reef zones. We summarise the results from our biological fiels studies in the open sea. 2. The biological investigations were concentrated on the area of the Atlantis II Deep. Benthos was sampled between 700-2000m. For comparison a few samples were also taken further north in the central Red Sea, and to east and west along the flanking deep terraces (500-1000m). Plankton studies covered the total water column above the Deep, and were extended along the axial through to north and south. 3. Benthos sampling was carried out using a heavy closing trawl, a large box grab (box size 50 × 50 cm), Van Veen grabs and traps; photographic surveys were made a phototrap and a photosled. Community respiration was measured with a ship-board method using grab subsamples. Nutrient concentrations, seston and phytoplankton standing stocks as well as in situ primary production were determined from hydrocast samples. Data on zooplankton and micronekton composition and standing stock were obtained from samples collected using different multiple opening-and-closing nets equipped with 100 μm, 300 μm, and 1000 μm mesh sizes. Daily and ontogenetical vertical migration patterns were studied by comparisons of data from midday and midnight tows. 4. Throughout the whole area the sediment is a pteropod ooze containing low contentrations of organic matter; measured organic carbon and nitrogen contents were 0.5 and 0.05% respectively, and chloroplastic pigment equivalents

  13. Modeling life the mathematics of biological systems

    CERN Document Server

    Garfinkel, Alan; Guo, Yina

    2017-01-01

    From predator-prey populations in an ecosystem, to hormone regulation within the body, the natural world abounds in dynamical systems that affect us profoundly. This book develops the mathematical tools essential for students in the life sciences to describe these interacting systems and to understand and predict their behavior. Complex feedback relations and counter-intuitive responses are common in dynamical systems in nature; this book develops the quantitative skills needed to explore these interactions. Differential equations are the natural mathematical tool for quantifying change, and are the driving force throughout this book. The use of Euler’s method makes nonlinear examples tractable and accessible to a broad spectrum of early-stage undergraduates, thus providing a practical alternative to the procedural approach of a traditional Calculus curriculum. Tools are developed within numerous, relevant examples, with an emphasis on the construction, evaluation, and interpretation of mathematical models ...

  14. Amoxicillin in a biological water recovery system

    International Nuclear Information System (INIS)

    Morse, A.; Jackson, A.; Rainwater, K.; Pickering, K.

    2002-01-01

    Pharmaceuticals are new contaminants of concern in the aquatic environment, having been identified in groundwater, surface water, and residential tap water. Possible sources of pharmaceuticals include household wastewaters, runoff from feedlots, or waste discharges from pharmaceutical manufacturing plants. When surface water or groundwater supplies impacted by pharmaceuticals are used in drinking water production, the contaminants may reduce drinking water quality. Many pharmaceuticals, such as amoxicillin, pass through the body largely unmetabolized and directly enter wastewater collection systems. Pharmaceuticals are designed to persist in the body long enough to have the desired therapeutic effect. Therefore, they may also have the ability to persist in the environment (Seiler et al, 1999). The purpose of this work is to determine the overall transformation potential of a candidate pharmaceutical in wastewater treatment with specific emphasis on recycle systems. Amoxicillin is the selected pharmaceutical agent, an orally absorbed broad-spectrum antibiotic with a variety of clinical uses including ear, nose, and throat infections and lower respiratory tract infections. Experiments were conducted using an anaerobic reactor (with NO 3 - and NO 2 - as the e - acceptors) followed by a two-phase nitrifying tubular reactor. Influent composed of water, urine and surfactant was spiked with amoxicillin and fed into the wastewater recycle system. The concentration of amoxicillin in the feed and effluent was quantified using an HPLC. Results from this study include potential for long-term buildup in recycled systems, accumulation of breakdown products and possible transfer of antibiotic resistance to microorganisms in the system effluent. In addition, the results of this study may provide information on contamination potential for communities that are considering supplementing drinking water supplies with recovered wastewater or for entities considering a closed loop

  15. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  16. Construction of a Linux based chemical and biological information system.

    Science.gov (United States)

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  17. Circadian systems biology: When time matters

    Directory of Open Access Journals (Sweden)

    Luise Fuhr

    2015-01-01

    In this manuscript we review the combination of experimental methodologies, bioinformatics and theoretical models that have been essential to explore this remarkable timing-system. Such an integrative and interdisciplinary approach may provide new strategies with regard to chronotherapeutic treatment and new insights concerning the restoration of the circadian timing in clock-associated diseases.

  18. Statistical Model Checking for Biological Systems

    DEFF Research Database (Denmark)

    David, Alexandre; Larsen, Kim Guldstrand; Legay, Axel

    2014-01-01

    Statistical Model Checking (SMC) is a highly scalable simulation-based verification approach for testing and estimating the probability that a stochastic system satisfies a given linear temporal property. The technique has been applied to (discrete and continuous time) Markov chains, stochastic...

  19. Imaging of the peripheral vascular system

    International Nuclear Information System (INIS)

    Gould, S.A.; Pond, G.D.; Pinsky, S.; Moss, G.S.; Srikantaswamy, S.; Ryo, U.Y.

    1984-01-01

    This book is limited neither to the peripheral vascular system nor to diagnostic imaging techniques. Its 18 chapters cover nonimaging blood-flow techniques (Doppler ultrasound, plethysmography) as well as noninvasive and invasive imaging techniques (ultrasound, computed tomography, radionuclide digital-subtraction angiography, and contrast angiography). These are applied not only to the peripheral vascular system but also to the aorta and vena cava

  20. Image digitizer system for bubble chamber laser

    International Nuclear Information System (INIS)

    Haggerty, H.

    1986-01-01

    An IBM PC-based image digitizer system has been assembled to monitor the laser flash used for holography at the 15 foot bubble chamber. The hardware and the operating software are outlined. For an operational test of the system, an array of LEDs was flashed with a 10 microsecond pulse and the image was grabbed by one of the operating programs and processed

  1. IDAPS (Image Data Automated Processing System) System Description

    Science.gov (United States)

    1988-06-24

    This document describes the physical configuration and components used in the image processing system referred to as IDAPS (Image Data Automated ... Processing System). This system was developed by the Environmental Research Institute of Michigan (ERIM) for Eglin Air Force Base. The system is designed

  2. 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).

  3. Advanced millimeter wave imaging systems

    Science.gov (United States)

    Schuchardt, J. M.; Gagliano, J. A.; Stratigos, J. A.; Webb, L. L.; Newton, J. M.

    1980-01-01

    Unique techniques are being utilized to develop self-contained imaging radiometers operating at single and multiple frequencies near 35, 95 and 183 GHz. These techniques include medium to large antennas for high spatial resolution, lowloss open structures for RF confinemnt and calibration, wide bandwidths for good sensitivity plus total automation of the unit operation and data collection. Applications include: detection of severe storms, imaging of motor vehicles, and the remote sensing of changes in material properties.

  4. 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

  5. Automated imaging system for single molecules

    Science.gov (United States)

    Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

    2012-09-18

    There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

  6. An online model composition tool for system biology models.

    Science.gov (United States)

    Coskun, Sarp A; Cicek, A Ercument; Lai, Nicola; Dash, Ranjan K; Ozsoyoglu, Z Meral; Ozsoyoglu, Gultekin

    2013-09-05

    There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user's input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.

  7. 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.

  8. Development of a THz spectroscopic imaging system

    International Nuclear Information System (INIS)

    Usami, M; Iwamoto, T; Fukasawa, R; Tani, M; Watanabe, M; Sakai, K

    2002-01-01

    We have developed a real-time THz imaging system based on the two-dimensional (2D) electro-optic (EO) sampling technique. Employing the 2D EO-sampling technique, we can obtain THz images using a CCD camera at a video rate of up to 30 frames per second. A spatial resolution of 1.4 mm was achieved. This resolution was reasonably close to the theoretical limit determined by diffraction. We observed not only static objects but also moving ones. To acquire spectroscopic information, time-domain images were collected. By processing these images on a computer, we can obtain spectroscopic images. Spectroscopy for silicon wafers was demonstrated

  9. Clinical software for MR imaging system, 4

    International Nuclear Information System (INIS)

    Shimizu, Koji; Kasai, Akira; Okamura, Shoichi

    1992-01-01

    Magnetic resonance imaging continues to elicit new application software through the recent technological advances of MR equipment. This paper describes several applications of our newly developed clinical software. The fast SE sequence (RISE) has proved to reduce routine examination time and to improve image quality, and ultra-fast FE sequence (SMASH) was found to extend the diagnostic capabilities in the field of cardiac study. Diffusion/perfusion imaging achieved in our MR system showed significant promise for providing novel information regarding tissue characterization. Furthermore, Image quality and practicalities of MR angiography have been improved by advanced imaging sequences and sophisticated post-processing software. (author)

  10. An integrated multimodality image-guided robot system for small-animal imaging research

    International Nuclear Information System (INIS)

    Hsu, Wen-Lin; Hsin Wu, Tung; Hsu, Shih-Ming; Chen, Chia-Lin; Lee, Jason J.S.; Huang, Yung-Hui

    2011-01-01

    We design and construct an image-guided robot system for use in small-animal imaging research. This device allows the use of co-registered small-animal PET-MRI images to guide the movements of robotic controllers, which will accurately place a needle probe at any predetermined location inside, for example, a mouse tumor, for biological readouts without sacrificing the animal. This system is composed of three major components: an automated robot device, a CCD monitoring mechanism, and a multimodality registration implementation. Specifically, the CCD monitoring mechanism was used for correction and validation of the robot device. To demonstrate the value of the proposed system, we performed a tumor hypoxia study that involved FMISO small-animal PET imaging and the delivering of a pO 2 probe into the mouse tumor using the image-guided robot system. During our evaluation, the needle positioning error was found to be within 0.153±0.042 mm of desired placement; the phantom simulation errors were within 0.693±0.128 mm. In small-animal studies, the pO 2 probe measurements in the corresponding hypoxia areas showed good correlation with significant, low tissue oxygen tensions (less than 6 mmHg). We have confirmed the feasibility of the system and successfully applied it to small-animal investigations. The system could be easily adapted to extend to other biomedical investigations in the future.

  11. Systematic integration of experimental data and models in systems biology.

    Science.gov (United States)

    Li, Peter; Dada, Joseph O; Jameson, Daniel; Spasic, Irena; Swainston, Neil; Carroll, Kathleen; Dunn, Warwick; Khan, Farid; Malys, Naglis; Messiha, Hanan L; Simeonidis, Evangelos; Weichart, Dieter; Winder, Catherine; Wishart, Jill; Broomhead, David S; Goble, Carole A; Gaskell, Simon J; Kell, Douglas B; Westerhoff, Hans V; Mendes, Pedro; Paton, Norman W

    2010-11-29

    The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

  12. Image quality of digital mammography images produced using wet and dry laser imaging systems

    International Nuclear Information System (INIS)

    Al Khalifah, K.; Brindhaban, A.; AlArfaj, R.; Jassim, O.

    2006-01-01

    Introduction: A study was carried out to compare the quality of digital mammographic images printed or processed by a wet laser imaging system and a dedicated mammographic dry laser imaging system. Material and methods: Digital images of a tissue equivalent breast phantom were obtained using a GE Senographe 2000D digital mammography system and different target/filter combinations of the X-ray tube. These images were printed on films using the Fuji FL-IM D wet laser imaging system and the Kodak DryView 8600 dry laser imaging system. The quality of images was assessed in terms of detectability of microcalcifications and simulated tumour masses by five radiologists. In addition, the contrast index and speed index of the two systems were measured using the step wedge in the phantom. The unpaired, unequal variance t-test was used to test any statistically significant differences. Results: There were no significant (p < 0.05) differences between the images printed using the two systems in terms of microcalcification and tumour mass detectability. The wet system resulted in slightly higher contrast index while the dry system showed significantly higher speed index. Conclusion: Both wet and dry laser imaging systems can produce mammography images of good quality on which 0.2 mm microcalcifications and 2 mm tumour masses can be detected. Dry systems are preferable due to the absence of wet chemical processing and solid or liquid chemical waste. The wet laser imaging systems, however, still represent a useful alternative to dry laser imaging systems for mammography studies

  13. Thermostability of biological systems: fundamentals, challenges, and quantification.

    Science.gov (United States)

    He, Xiaoming

    2011-01-01

    This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems.

  14. Standards, Data Exchange and Intellectual Property Rights in Systems Biology

    DEFF Research Database (Denmark)

    van Zimmeren, Esther; Rutz, Berthold; Minssen, Timo

    2016-01-01

    ” of scientists. In 2015, Biotechnology Journal published a report from an expert meeting on “Synthetic Biology & Intellectual Property Rights” organized by the Danish Agency for Science, Technology and Innovation sponsored by the European Research Area Network (ERA-Net) in Synthetic Biology (ERASynBio), in which...... we provided a number of recommendations for a variety of stakeholders. The current article offers some deeper reflections about the interface between IPRs, standards and data exchange in Systems Biology resulting from an Expert Meeting funded by another ERA-Net, ERASysAPP. The meeting brought...... together experts and stakeholders (e.g. scientists, company representatives, officials from public funding organizations) in systems biology (SysBio) from different countries.  Despite the different profiles of the stakeholders at the meeting and the variety of interests, many concerns and opinions were...

  15. Three-dimensional printing of human skeletal muscle cells: An interdisciplinary approach for studying biological systems.

    Science.gov (United States)

    Bagley, James R; Galpin, Andrew J

    2015-01-01

    Interdisciplinary exploration is vital to education in the 21st century. This manuscript outlines an innovative laboratory-based teaching method that combines elements of biochemistry/molecular biology, kinesiology/health science, computer science, and manufacturing engineering to give students the ability to better conceptualize complex biological systems. Here, we utilize technology available at most universities to print three-dimensional (3D) scale models of actual human muscle cells (myofibers) out of bioplastic materials. The same methodological approach could be applied to nearly any cell type or molecular structure. This advancement is significant because historically, two-dimensional (2D) myocellular images have proven insufficient for detailed analysis of organelle organization and morphology. 3D imaging fills this void by providing accurate and quantifiable myofiber structural data. Manipulating tangible 3D models combats 2D limitation and gives students new perspectives and alternative learning experiences that may assist their understanding. This approach also exposes learners to 1) human muscle cell extraction and isolation, 2) targeted fluorescence labeling, 3) confocal microscopy, 4) image processing (via open-source software), and 5) 3D printing bioplastic scale-models (×500 larger than the actual cells). Creating these physical models may further student's interest in the invisible world of molecular and cellular biology. Furthermore, this interdisciplinary laboratory project gives instructors of all biological disciplines a new teaching tool to foster integrative thinking. © 2015 The International Union of Biochemistry and Molecular Biology.

  16. Applications of dynamical systems in biology and medicine

    CERN Document Server

    Radunskaya, Ami

    2015-01-01

    This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

  17. Biological indicators for monitoring water quality of MTF canals system

    Science.gov (United States)

    Sethi, S. L.

    1975-01-01

    Biological models, diversity indexes, were developed to predict environmental effects of NASA's Mississippi test facility (MTF) chemical operations on canal systems in the area. To predict the effects on local streams, a physical model of unpolluted streams was established. The model is fed by artesian well water free of background levels of pollutants. The species diversity and biota composition of unpolluted MTF stream was determined; resulting information will be used to form baseline data for future comparisons. Biological modeling was accomplished by adding controlled quantities or kinds of chemical pollutants and evaluating the effects of these chemicals on the biological life of the stream.

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

    International Nuclear Information System (INIS)

    Martinez E, J. C.; Cordova F, T.; Hugo R, V.

    2015-10-01

    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)

  19. 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)

  20. Thermoluminescence dosimetry in quality imaging in CR mammography systems

    Energy Technology Data Exchange (ETDEWEB)

    Gaona, E.; Franco E, J.G. [UAM-Xochimilco, 04960 Mexico D.F. (Mexico); Azorin N, J. [UAM-Iztapalapa, 09340 Mexico D.F. (Mexico); Diaz G, J.A.I. [CICATA, Unidad Legaria, Av. Legaria 694, 11599 mexico D.F. (Mexico); Arreola, M. [Department of Radiology, Shands Hospital at UF, PO Box 100374, Gainesville, FL 32610-0374 (United States)

    2006-07-01

    The aim of this work is to estimate the average glandular dose with Thermoluminescence Dosimetry (TLD) and comparison with quality imaging in CR mammography. For measuring dose, FDA and ACR use a phantom, so that dose and image quality are assessed with the same test object. The mammography is a radiological image to visualize early biological manifestations of breast cancer. Digital systems have two types of image-capturing devices, Full Field Digital Mammography (FFDM) and CR mammography. In Mexico, there are several CR mammography systems in clinical use, but only one CR mammography system has been approved for use by the FDA. Mammography CR uses a photostimulable phosphor detector (PSP) system. Most CR plates are made of 85% BaFBr and 15% BaFI doped with europium (Eu) commonly called barium fluoro halide. We carry out an exploratory survey of six CR mammography units from three different manufacturers and six dedicated x-ray mammography units with fully automatic exposure. The results show three CR mammography units (50%) have a dose that overcomes 3.0 mGy and it doesn't improve the image quality and dose to the breast will be excessive. The differences between doses averages from TLD system and dosimeter with ionization chamber are less than 10%. TLD system is a good option for average glandular dose measurement. (Author)

  1. Thermoluminescence dosimetry in quality imaging in CR mammography systems

    International Nuclear Information System (INIS)

    Gaona, E.; Franco E, J.G.; Azorin N, J.; Diaz G, J.A.I.; Arreola, M.

    2006-01-01

    The aim of this work is to estimate the average glandular dose with Thermoluminescence Dosimetry (TLD) and comparison with quality imaging in CR mammography. For measuring dose, FDA and ACR use a phantom, so that dose and image quality are assessed with the same test object. The mammography is a radiological image to visualize early biological manifestations of breast cancer. Digital systems have two types of image-capturing devices, Full Field Digital Mammography (FFDM) and CR mammography. In Mexico, there are several CR mammography systems in clinical use, but only one CR mammography system has been approved for use by the FDA. Mammography CR uses a photostimulable phosphor detector (PSP) system. Most CR plates are made of 85% BaFBr and 15% BaFI doped with europium (Eu) commonly called barium fluoro halide. We carry out an exploratory survey of six CR mammography units from three different manufacturers and six dedicated x-ray mammography units with fully automatic exposure. The results show three CR mammography units (50%) have a dose that overcomes 3.0 mGy and it doesn't improve the image quality and dose to the breast will be excessive. The differences between doses averages from TLD system and dosimeter with ionization chamber are less than 10%. TLD system is a good option for average glandular dose measurement. (Author)

  2. Systems-biology dissection of eukaryotic cell growth

    Directory of Open Access Journals (Sweden)

    Andrews Justen

    2010-05-01

    Full Text Available Abstract A recent article in BMC Biology illustrates the use of a systems-biology approach to integrate data across the transcriptome, proteome and metabolome of budding yeast in order to dissect the relationship between nutrient conditions and cell growth. See research article http://jbiol.com/content/6/2/4 and http://www.biomedcentral.com/1741-7007/8/68

  3. Nuclear magnetic resonance studies of biological systems

    International Nuclear Information System (INIS)

    Antypas, W.G. Jr.

    1988-01-01

    The difference between intracellular and extracellular proton relaxation rates provides the basis for the determination of the mean hemoglobin concentration (MHC) in red blood cells. The observed water T 1 relaxation data from red blood cell samples under various conditions were fit to the complete equation for the time-dependent decay of magnetization for a two-compartment system including chemical exchange. The MHC for each sample was calculated from the hematocrit and the intracellular water fraction as determined by NMR. The binding of the phosphorylcholine (PC) analogue, 2-(trimethylphosphonio)-ethylphosphate (phosphoryl-phosphocholine, PPC) to the PC binding myeloma proteins TEPC-15, McPC 603, and MOPC 167 was studied by 31 P NMR

  4. Modeling of biological intelligence for SCM system optimization.

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  5. Dietary antioxidant synergy in chemical and biological systems.

    Science.gov (United States)

    Wang, Sunan; Zhu, Fan

    2017-07-24

    Antioxidant (AOX) synergies have been much reported in chemical ("test-tube" based assays focusing on pure chemicals), biological (tissue culture, animal and clinical models), and food systems during the past decade. Tentative synergies differ from each other due to the composition of AOX and the quantification methods. Regeneration mechanism responsible for synergy in chemical systems has been discussed. Solvent effects could contribute to the artifacts of synergy observed in the chemical models. Synergy in chemical models may hardly be relevant to biological systems that have been much less studied. Apparent discrepancies exist in understanding the molecular mechanisms in both chemical and biological systems. This review discusses diverse variables associated with AOX synergy and molecular scenarios for explanation. Future research to better utilize the synergy is suggested.

  6. Modeling of Biological Intelligence for SCM System Optimization

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

  7. Modeling of Biological Intelligence for SCM System Optimization

    Science.gov (United States)

    Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

    2012-01-01

    This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

  8. Tritium isotope fractionation in biological systems and in analytical procedures

    International Nuclear Information System (INIS)

    Kim, M.A.; Baumgaertner, Franz

    1989-01-01

    The organically bound tritium (OBT) is evaluated in biological systems by determining the tritium distribution ratio (R-value), i.e. tritium concentrations in organic substance to cell water. The determination of the R-value always involves isotope fractionation is applied analytical procedures and hence the evaluation of the true OBT -value in a given biological system appears more complicated than hitherto known in the literature. The present work concentrates on the tritium isotope fractionation in the cell water separation and on the resulting effects on the R-value. The analytical procedures examined are vacuum freeze drying under equilibrium and non-equilibrium conditions and azeotropic distillation. The vaporization isotope effects are determined separately in the phase transition of solid or liquid to gas in pure tritium water systems as well as in real biological systems, e.g. corn plant. The results are systematically analyzed and the influence of isotope effects on the R-value is rigorously quantified

  9. Vibrational resonances in biological systems at microwave frequencies.

    Science.gov (United States)

    Adair, Robert K

    2002-03-01

    Many biological systems can be expected to exhibit resonance behavior involving the mechanical vibration of system elements. The natural frequencies of such resonances will, generally, be in the microwave frequency range. Some of these systems will be coupled to the electromagnetic field by the charge distributions they carry, thus admitting the possibility that microwave exposures may generate physiological effects in man and other species. However, such microwave excitable resonances are expected to be strongly damped by interaction with their aqueous biological environment. Although those dissipation mechanisms have been studied, the limitations on energy transfers that follow from the limited coupling of these resonances to the electromagnetic field have not generally been considered. We show that this coupling must generally be very small and thus the absorbed energy is so strongly limited that such resonances cannot affect biology significantly even if the systems are much less strongly damped than expected from basic dissipation models.

  10. Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

    Science.gov (United States)

    Tsou, Ann-Ping; Sun, Yi-Ming; Liu, Chia-Lin; Huang, Hsien-Da; Horng, Jorng-Tzong; Tsai, Meng-Feng; Liu, Baw-Juine

    2006-07-01

    Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.

  11. Investigating cholesterol metabolism and ageing using a systems biology approach.

    Science.gov (United States)

    Morgan, A E; Mooney, K M; Wilkinson, S J; Pickles, N A; Mc Auley, M T

    2017-08-01

    CVD accounted for 27 % of all deaths in the UK in 2014, and was responsible for 1·7 million hospital admissions in 2013/2014. This condition becomes increasingly prevalent with age, affecting 34·1 and 29·8 % of males and females over 75 years of age respectively in 2011. The dysregulation of cholesterol metabolism with age, often observed as a rise in LDL-cholesterol, has been associated with the pathogenesis of CVD. To compound this problem, it is estimated by 2050, 22 % of the world's population will be over 60 years of age, in culmination with a growing resistance and intolerance to pre-existing cholesterol regulating drugs such as statins. Therefore, it is apparent research into additional therapies for hypercholesterolaemia and CVD prevention is a growing necessity. However, it is also imperative to recognise this complex biological system cannot be studied using a reductionist approach; rather its biological uniqueness necessitates a more integrated methodology, such as that offered by systems biology. In this review, we firstly discuss cholesterol metabolism and how it is affected by diet and the ageing process. Next, we describe therapeutic strategies for hypercholesterolaemia, and finally how the systems biology paradigm can be utilised to investigate how ageing interacts with complex systems such as cholesterol metabolism. We conclude by emphasising the need for nutritionists to work in parallel with the systems biology community, to develop novel approaches to studying cholesterol metabolism and its interaction with ageing.

  12. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  13. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian; Ihekwaba, Adoha

    2007-01-01

    A. Ihekwaba, R. Mardare. A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems. Case study: NFkB system. In Proc. of International Conference of Computational Methods in Sciences and Engineering (ICCMSE), American Institute of Physics, AIP Proceedings, N 2...

  14. Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

    DEFF Research Database (Denmark)

    Chang, Roger L.; Andrews, Kathleen; Kim, Donghyuk

    2013-01-01

    Improve the System A "systems biology" approach may clarify, for example, how particular proteins determine sensitivity of bacteria to extremes of temperature. Chang et al. (p. 1220) integrated information on protein structure with a model of metabolism, thus associating the protein structure of ...

  15. Hepatocellular carcinoma: a systems biology perspective

    Directory of Open Access Journals (Sweden)

    Lorenza Alice D'alessandro

    2013-02-01

    Full Text Available Hepatocellular carcinomas (HCC have different etiology and heterogenic genomic alterations lead to high complexity. The molecular features of HCC have largely been studied by gene expression and proteome profiling focusing on the correlations between the expression of specific markers and clinical data. Integration of the increasing amounts of data in databases has facilitated the link of genomic and proteomic profiles of HCC to disease state and clinical outcome. Despite the current knowledge, specific molecular markers remain to be identified and new strategies are required to establish novel targeted therapies. In the last years, mathematical models reconstructing gene and protein networks based on experimental data of HCC have been developed providing powerful tools to predict candidate interactions and potential targets for therapy. Furthermore, the combination of dynamic and logical mathematical models with quantitative data allows detailed mechanistic insights into system properties. To address effects at the organ level, mathematical models reconstructing the three-dimensional organization of liver lobules were developed. In the future, integration of different modeling approaches capturing the effects at the cellular up to the organ level is required to address the complex properties of HCC and to enable the discovery of new targets for HCC prevention or treatment.

  16. Lossy image compression for digital medical imaging systems

    Science.gov (United States)

    Wilhelm, Paul S.; Haynor, David R.; Kim, Yongmin; Nelson, Alan C.; Riskin, Eve A.

    1990-07-01

    Image compression at rates of 10:1 or greater could make PACS much more responsive and economically attractive. This paper describes a protocol for subjective and objective evaluation of the fidelity of compressed/decompressed images to the originals and presents the results ofits application to four representative and promising compression methods. The methods examined are predictive pruned tree-structured vector quantization, fractal compression, the discrete cosine transform with equal weighting of block bit allocation, and the discrete cosine transform with human visual system weighting of block bit allocation. Vector quantization is theoretically capable of producing the best compressed images, but has proven to be difficult to effectively implement. It has the advantage that it can reconstruct images quickly through a simple lookup table. Disadvantages are that codebook training is required, the method is computationally intensive, and achieving the optimum performance would require prohibitively long vector dimensions. Fractal compression is a relatively new compression technique, but has produced satisfactory results while being computationally simple. It is fast at both image compression and image reconstruction. Discrete cosine iransform techniques reproduce images well, but have traditionally been hampered by the need for intensive computing to compress and decompress images. A protocol was developed for side-by-side observer comparison of reconstructed images with originals. Three 1024 X 1024 CR (Computed Radiography) images and two 512 X 512 X-ray CT images were viewed at six bit rates (0.2, 0.4, 0.6, 0.9, 1.2, and 1.5 bpp for CR, and 1.0, 1.3, 1.6, 1.9, 2.2, 2.5 bpp for X-ray CT) by nine radiologists at the University of Washington Medical Center. The CR images were viewed on a Pixar II Megascan (2560 X 2048) monitor and the CT images on a Sony (1280 X 1024) monitor. The radiologists' subjective evaluations of image fidelity were compared to

  17. Advances in study of molecular imaging reporte gene systems

    International Nuclear Information System (INIS)

    Wu Tao; An Rui

    2010-01-01

    The use of molecular imaging reporter gene systems has allowed gene therapy to move from the laboratory to the clinical application, which provides methodology to monitor the expression of therapeutic gene noninvasively and achieve quantitative outcome in vivo. Recently, the radionuclide reporter gene still is the focus many studies, but MRI and optical reporter gene have gradually played a important part in reporter gene systems. On the basis of combination of multi-subject, for example applied chemistry and molecular biology, more and more new modified reporter genes and molecular probes have spread out. This paper mainly introduces the advantages and disadvantages of reporter gene system and development trends. (authors)

  18. SEEK: a systems biology data and model management platform.

    Science.gov (United States)

    Wolstencroft, Katherine; Owen, Stuart; Krebs, Olga; Nguyen, Quyen; Stanford, Natalie J; Golebiewski, Martin; Weidemann, Andreas; Bittkowski, Meik; An, Lihua; Shockley, David; Snoep, Jacky L; Mueller, Wolfgang; Goble, Carole

    2015-07-11

    Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and

  19. A gamma cammera image processing system

    International Nuclear Information System (INIS)

    Chen Weihua; Mei Jufang; Jiang Wenchuan; Guo Zhenxiang

    1987-01-01

    A microcomputer based gamma camera image processing system has been introduced. Comparing with other systems, the feature of this system is that an inexpensive microcomputer has been combined with specially developed hardware, such as, data acquisition controller, data processor and dynamic display controller, ect. Thus the process of picture processing has been speeded up and the function expense ratio of the system raised

  20. Advanced image display systems in radiology

    International Nuclear Information System (INIS)

    Wendler, T.

    1987-01-01

    Advanced image display systems for the fully digital diagnostic imaging departments of the future will be far more than simple replacements of the traditional film-viewing equipment. The new capabilities of very high resolution and highly dynamic displays offer a userfriendly and problem-oriented way of image interpretation. Advanced harware-, software- and human-machine interaction-concepts have been outlined. A scenario for a future way of handling and displaying images, reflecting a new image viewing paradigm in radiology is sketched which has been realized in an experimental image workstation model in the laboratory which, despite its technical complexity, offers a consistent strategy for fast and convenient interaction with image objects. The perspective of knowledge based techniques for workstation control software with object-oriented programming environments and user- and task-adaptive behavior leads to more advanced display properties and a new quality of userfriendliness. 2 refs.; 5 figs

  1. Imaging modes of atomic force microscopy for application in molecular and cell biology.

    Science.gov (United States)

    Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

    2017-04-06

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

  2. MONSOON Image Acquisition System | CTIO

    Science.gov (United States)

    Staff CTIO History CTIO Directors Historic Highlights Site Description Contact Us Astronomers Observing Contact Acknowledgments TS4 History ISPI ISPI Exposure Time Calculator OSIRIS Spartan Optical Imagers single detector to very large focal planes made from arrays of detectors. The basic hierarchy of a

  3. Devices for Evaluating Imaging Systems. Chapter 15

    Energy Technology Data Exchange (ETDEWEB)

    Demirkaya, O.; Al-Mazrou, R. [Department of Biomedical Physics, King Faisal Specialist Hospital and Research Centre, Riyadh (Saudi Arabia)

    2014-12-15

    A quality management system (QMS) has three main components: (a) Quality assurance (QA); (b) Quality improvement; (c) Quality control (QC). The aim of a QMS is to ensure that the deliverables meet the requirements set forth by the users. The deliverables can be, in general, all the services provided in a nuclear medicine department, and the diagnostic imaging services in particular. In this section, the primary focus is the diagnostic imaging equipment and images produced by them.

  4. Imaging of dopaminergic system in movement disorders

    International Nuclear Information System (INIS)

    Kim, Yu Kyeong; Kim, Sang Eun

    2007-01-01

    Parkinson's disease is a common neurodegenerative disorder that is mainly caused by dopaminergic neuron loss in the substantia nigra. Several radiopharmaceutics have been developed to evaluated the integrity of dopaminergic neuronal system. In vivo PET and SPECT imaging of presynaptic dopamine imaging are already applied to Parkinson's disease and other parkinsonism, and can demonstrate the dopaminergic dysfunction. This review summarized the use of the presynaptic dopaminergic imaging in PD as biomarkers in evaluation of disease progression as well as in diagnosis of PD

  5. Scanned Image Projection System Employing Intermediate Image Plane

    Science.gov (United States)

    DeJong, Christian Dean (Inventor); Hudman, Joshua M. (Inventor)

    2014-01-01

    In imaging system, a spatial light modulator is configured to produce images by scanning a plurality light beams. A first optical element is configured to cause the plurality of light beams to converge along an optical path defined between the first optical element and the spatial light modulator. A second optical element is disposed between the spatial light modulator and a waveguide. The first optical element and the spatial light modulator are arranged such that an image plane is created between the spatial light modulator and the second optical element. The second optical element is configured to collect the diverging light from the image plane and collimate it. The second optical element then delivers the collimated light to a pupil at an input of the waveguide.

  6. Synthetic and systems biology for microbial production of commodity chemicals.

    Science.gov (United States)

    Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J; Keasling, Jay D; Martín, Héctor García

    2016-01-01

    The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

  7. Continuum analysis of biological systems conserved quantities, fluxes and forces

    CERN Document Server

    Suraishkumar, G K

    2014-01-01

    This book addresses the analysis, in the continuum regime, of biological systems at various scales, from the cellular level to the industrial one. It presents both fundamental conservation principles (mass, charge, momentum and energy) and relevant fluxes resulting from appropriate driving forces, which are important for the analysis, design and operation of biological systems. It includes the concept of charge conservation, an important principle for biological systems that is not explicitly covered in any other book of this kind. The book is organized in five parts: mass conservation; charge conservation; momentum conservation; energy conservation; and multiple conservations simultaneously applied. All mathematical aspects are presented step by step, allowing any reader with a basic mathematical background (calculus, differential equations, linear algebra, etc.) to follow the text with ease. The book promotes an intuitive understanding of all the relevant principles and in so doing facilitates their applica...

  8. Learning (from) the errors of a systems biology model.

    Science.gov (United States)

    Engelhardt, Benjamin; Frőhlich, Holger; Kschischo, Maik

    2016-02-11

    Mathematical modelling is a labour intensive process involving several iterations of testing on real data and manual model modifications. In biology, the domain knowledge guiding model development is in many cases itself incomplete and uncertain. A major problem in this context is that biological systems are open. Missed or unknown external influences as well as erroneous interactions in the model could thus lead to severely misleading results. Here we introduce the dynamic elastic-net, a data driven mathematical method which automatically detects such model errors in ordinary differential equation (ODE) models. We demonstrate for real and simulated data, how the dynamic elastic-net approach can be used to automatically (i) reconstruct the error signal, (ii) identify the target variables of model error, and (iii) reconstruct the true system state even for incomplete or preliminary models. Our work provides a systematic computational method facilitating modelling of open biological systems under uncertain knowledge.

  9. Image processing system for flow pattern measurements

    International Nuclear Information System (INIS)

    Ushijima, Satoru; Miyanaga, Yoichi; Takeda, Hirofumi

    1989-01-01

    This paper describes the development and application of an image processing system for measurements of flow patterns occuring in natural circulation water flows. In this method, the motions of particles scattered in the flow are visualized by a laser light slit and they are recorded on normal video tapes. These image data are converted to digital data with an image processor and then transfered to a large computer. The center points and pathlines of the particle images are numerically analized, and velocity vectors are obtained with these results. In this image processing system, velocity vectors in a vertical plane are measured simultaneously, so that the two dimensional behaviors of various eddies, with low velocity and complicated flow patterns usually observed in natural circulation flows, can be determined almost quantitatively. The measured flow patterns, which were obtained from natural circulation flow experiments, agreed with photographs of the particle movements, and the validity of this measuring system was confirmed in this study. (author)

  10. Advances in Structural Biology and the Application to Biological Filament Systems.

    Science.gov (United States)

    Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

    2018-04-01

    Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

  11. Optical Imaging Sensors and Systems for Homeland Security Applications

    CERN Document Server

    Javidi, Bahram

    2006-01-01

    Optical and photonic systems and devices have significant potential for homeland security. Optical Imaging Sensors and Systems for Homeland Security Applications presents original and significant technical contributions from leaders of industry, government, and academia in the field of optical and photonic sensors, systems and devices for detection, identification, prevention, sensing, security, verification and anti-counterfeiting. The chapters have recent and technically significant results, ample illustrations, figures, and key references. This book is intended for engineers and scientists in the relevant fields, graduate students, industry managers, university professors, government managers, and policy makers. Advanced Sciences and Technologies for Security Applications focuses on research monographs in the areas of -Recognition and identification (including optical imaging, biometrics, authentication, verification, and smart surveillance systems) -Biological and chemical threat detection (including bios...

  12. Glycoengineering in CHO cells: Advances in systems biology

    DEFF Research Database (Denmark)

    Tejwani, Vijay; Andersen, Mikael Rørdam; Nam, Jong Hyun

    2018-01-01

    are not well understood. A systems biology approach combining different technologies is needed for complete understanding of the molecular processes accounting for this variability and to open up new venues in cell line development. In this review, we describe several advances in genetic manipulation, modeling......For several decades, glycoprotein biologics have been successfully produced from Chinese hamster ovary (CHO) cells. The therapeutic efficacy and potency of glycoprotein biologics are often dictated by their post translational modifications, particularly glycosylation, which unlike protein synthesis....... Recently, CHO cells have also been explored for production of therapeutic glycosaminoglycans (e.g. heparin), which presents similar challenges as producing glycoproteins biologics. Approaches to controlling heterogeneity in CHO cells and directing the biosynthetic process toward desired glycoforms...

  13. Fibre laser based broadband THz imaging systems

    DEFF Research Database (Denmark)

    Eichhorn, Finn

    imaging techniques. This thesis exhibits that fiber technology can improve the robustness and the flexibility of terahertz imaging systems both by the use of fiber-optic light sources and the employment of optical fibers as light distribution medium. The main focus is placed on multi-element terahertz...

  14. Image based rendering of iterated function systems

    NARCIS (Netherlands)

    Wijk, van J.J.; Saupe, D.

    2004-01-01

    A fast method to generate fractal imagery is presented. Iterated function systems (IFS) are based on repeatedly copying transformed images. We show that this can be directly translated into standard graphics operations: Each image is generated by texture mapping and blending copies of the previous

  15. Optical sensors and their applications for probing biological systems

    DEFF Research Database (Denmark)

    Palanco, Marta Espina

    There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant and mammal......There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant...... of a trapped cell. The project could provide new insights into the desired biosensor for future membrane-protein cell studies....

  16. The Systems Biology Research Tool: evolvable open-source software

    OpenAIRE

    Wright, J; Wagner, A

    2008-01-01

    Abstract Background Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput) experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level. Results We introduce a free, easy-to-use, open-source, integrated software platform calle...

  17. Sampling system for in vivo ultrasound images

    DEFF Research Database (Denmark)

    Jensen, Jorgen Arendt; Mathorne, Jan

    1991-01-01

    Newly developed algorithms for processing medical ultrasound images use the high frequency sampled transducer signal. This paper describes demands imposed on a sampling system suitable for acquiring such data and gives details about a prototype constructed. It acquires full clinical images...... at a sampling frequency of 20 MHz with a resolution of 12 bits. The prototype can be used for real time image processing. An example of a clinical in vivo image is shown and various aspects of the data acquisition process are discussed....

  18. Systems Biology of Meridians, Acupoints, and Chinese Herbs in Disease

    Directory of Open Access Journals (Sweden)

    Li-Ling Lin

    2012-01-01

    Full Text Available Meridians, acupoints, and Chinese herbs are important components of traditional Chinese medicine (TCM. They have been used for disease treatment and prevention and as alternative and complementary therapies. Systems biology integrates omics data, such as transcriptional, proteomic, and metabolomics data, in order to obtain a more global and complete picture of biological activity. To further understand the existence and functions of the three components above, we reviewed relevant research in the systems biology literature and found many recent studies that indicate the value of acupuncture and Chinese herbs. Acupuncture is useful in pain moderation and relieves various symptoms arising from acute spinal cord injury and acute ischemic stroke. Moreover, Chinese herbal extracts have been linked to wound repair, the alleviation of postmenopausal osteoporosis severity, and anti-tumor effects, among others. Different acupoints, variations in treatment duration, and herbal extracts can be used to alleviate various symptoms and conditions and to regulate biological pathways by altering gene and protein expression. Our paper demonstrates how systems biology has helped to establish a platform for investigating the efficacy of TCM in treating different diseases and improving treatment strategies.

  19. Collaborative Systems Biology Projects for the Military Medical Community.

    Science.gov (United States)

    Zalatoris, Jeffrey J; Scheerer, Julia B; Lebeda, Frank J

    2017-09-01

    This pilot study was conducted to examine, for the first time, the ongoing systems biology research and development projects within the laboratories and centers of the U.S. Army Medical Research and Materiel Command (USAMRMC). The analysis has provided an understanding of the breadth of systems biology activities, resources, and collaborations across all USAMRMC subordinate laboratories. The Systems Biology Collaboration Center at USAMRMC issued a survey regarding systems biology research projects to the eight U.S.-based USAMRMC laboratories and centers in August 2016. This survey included a data call worksheet to gather self-identified project and programmatic information. The general topics focused on the investigators and their projects, on the project's research areas, on omics and other large data types being collected and stored, on the analytical or computational tools being used, and on identifying intramural (i.e., USAMRMC) and extramural collaborations. Among seven of the eight laboratories, 62 unique systems biology studies were funded and active during the final quarter of fiscal year 2016. Of 29 preselected medical Research Task Areas, 20 were associated with these studies, some of which were applicable to two or more Research Task Areas. Overall, studies were categorized among six general types of objectives: biological mechanisms of disease, risk of/susceptibility to injury or disease, innate mechanisms of healing, diagnostic and prognostic biomarkers, and host/patient responses to vaccines, and therapeutic strategies including host responses to therapies. We identified eight types of omics studies and four types of study subjects. Studies were categorized on a scale of increasing complexity from single study subject/single omics technology studies (23/62) to studies integrating results across two study subject types and two or more omics technologies (13/62). Investigators at seven USAMRMC laboratories had collaborations with systems biology experts

  20. Teaching the physics of medical imaging: an active learning approach involving imaging of biological tissue

    DEFF Research Database (Denmark)

    Wilhjelm, Jens E.; Pihl, Michael Johannes; Lonsdale, Markus Nowak

    2008-01-01

    Introduction to medical imaging is an experimentally oriented course in the physics of medical imaging, where the students record, process and analyse 3D data of an unknown piece of formalin fixed animal tissue embedded in agar in order to estimate the tissue types present. Planar X-ray, CT, MRI......, ultrasound and SPECT/PET images are recorded, showing the tissue in very different ways. In order for the students to estimate the tissue type, they need to study the physical principles of the imaging modalities. The “true” answer is subsequently revealed by slicing the tissue....

  1. Four-Mirror Freeform Reflective Imaging Systems

    Data.gov (United States)

    National Aeronautics and Space Administration — Central Objectives: The research involves a revelation of the solution space for revolutionary families of four-mirror freeform reflective imaging systems. A...

  2. Fusion of Images from Dissimilar Sensor Systems

    National Research Council Canada - National Science Library

    Chow, Khin

    2004-01-01

    Different sensors exploit different regions of the electromagnetic spectrum; therefore a multi-sensor image fusion system can take full advantage of the complementary capabilities of individual sensors in the suit...

  3. Shimadzu magnetic resonance imaging system, SMT-50

    International Nuclear Information System (INIS)

    Oikawa, Shiro; Nishida, Takayuki; Fujio, Yasuo

    1986-01-01

    The magnetic resonance imaging (MRI) system, as a new modality of medical imaging, has already been put to practical applications on many clinical sites, through which a lot of clinical data has been accumulated. It can offer a powerful new probe of internal anatomy of the human body and its functions. Now that the MRI has established its effectiveness in diagnosis, a really practical MRI system which features high efficiency and economical design with high patient throughput is strongly called for. Introduced in this article is a superconductive magnet MRI system, SMT-50, operating at 5000 Gauss. It has realized an excellent diagnostic capability with such functions as multi-slice multi-echo imaging, high sensitive, surface coil technique and so on. High resolution image display (1024 x 1024 pixcel) unit and separate console system (viewing console and scanning console) will assist high patient throughput. The outline of the SMT-50 and its clinical data are reported here. (author)

  4. Imaging modes of atomic force microscopy for application in molecular and cell biology

    NARCIS (Netherlands)

    Dufrêne, Yves F.; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, A.H.; Gerber, Christoph; Müller, Daniel J.

    2017-01-01

    Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM

  5. 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.

  6. Improvements in the measurement system of a biological Magnetic Induction Tomographical experimental setup

    International Nuclear Information System (INIS)

    Bras, N. B.; Martins, R. C.; Serra, A. C.

    2010-01-01

    Magnetic Induction Tomography (MIT) is an imaging technique that allows mapping the internal structure complex conductivity of a body. In this paper a feasibility study to implement a higher resolution MIT system for biological tissues is carried out. Recent improvements in measured signal stability and accuracy as well as a much improved angular resolution measurement of the multi-coil setup are presented which, together with a new mechanical design allows obtaining longer stable and more accurate acquisitions. This allows improving the number of measurements without trends or external perturbations, leading to a better conductivity resolution and to an enhanced image reconstruction. Throughout the paper experimental data is used to consolidate results.

  7. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  8. System for imaging plutonium through heavy shielding

    International Nuclear Information System (INIS)

    Kuckertz, T.H.; Cannon, T.M.; Fenimore, E.E.; Moss, C.E.; Nixon, K.V.

    1984-04-01

    A single pinhole can be used to image strong self-luminescent gamma-ray sources such as plutonium on gamma scintillation (Anger) cameras. However, if the source is weak or heavily shielded, a poor signal to noise ratio can prevent acquisition of the image. An imaging system designed and built at Los Alamos National Laboratory uses a coded aperture to image heavily shielded sources. The paper summarizes the mathematical techniques, based on the Fast Delta Hadamard transform, used to decode raw images. Practical design considerations such as the phase of the uniformly redundant aperture and the encoded image sampling are discussed. The imaging system consists of a custom designed m-sequence coded aperture, a Picker International Corporation gamma scintillation camera, a LeCroy 3500 data acquisition system, and custom imaging software. The paper considers two sources - 1.5 mCi 57 Co unshielded at a distance of 27 m and 220 g of bulk plutonium (11.8% 240 Pu) with 0.3 cm lead, 2.5 cm steel, and 10 cm of dense plastic material at a distance of 77.5 cm. Results show that the location and geometry of a source hidden in a large sealed package can be determined without having to open the package. 6 references, 4 figures

  9. Systems Biology, Systems Medicine, Systems Pharmacology: The What and The Why.

    Science.gov (United States)

    Stéphanou, Angélique; Fanchon, Eric; Innominato, Pasquale F; Ballesta, Annabelle

    2018-05-09

    Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences.

  10. A distributed approach for parameters estimation in System Biology models

    International Nuclear Information System (INIS)

    Mosca, E.; Merelli, I.; Alfieri, R.; Milanesi, L.

    2009-01-01

    Due to the lack of experimental measurements, biological variability and experimental errors, the value of many parameters of the systems biology mathematical models is yet unknown or uncertain. A possible computational solution is the parameter estimation, that is the identification of the parameter values that determine the best model fitting respect to experimental data. We have developed an environment to distribute each run of the parameter estimation algorithm on a different computational resource. The key feature of the implementation is a relational database that allows the user to swap the candidate solutions among the working nodes during the computations. The comparison of the distributed implementation with the parallel one showed that the presented approach enables a faster and better parameter estimation of systems biology models.

  11. Document Examination: Applications of Image Processing Systems.

    Science.gov (United States)

    Kopainsky, B

    1989-12-01

    Dealing with images is a familiar business for an expert in questioned documents: microscopic, photographic, infrared, and other optical techniques generate images containing the information he or she is looking for. A recent method for extracting most of this information is digital image processing, ranging from the simple contrast and contour enhancement to the advanced restoration of blurred texts. When combined with a sophisticated physical imaging system, an image pricessing system has proven to be a powerful and fast tool for routine non-destructive scanning of suspect documents. This article reviews frequent applications, comprising techniques to increase legibility, two-dimensional spectroscopy (ink discrimination, alterations, erased entries, etc.), comparison techniques (stamps, typescript letters, photo substitution), and densitometry. Computerized comparison of handwriting is not included. Copyright © 1989 Central Police University.

  12. A fractal-based image encryption system

    KAUST Repository

    Abd-El-Hafiz, S. K.

    2014-12-01

    This study introduces a novel image encryption system based on diffusion and confusion processes in which the image information is hidden inside the complex details of fractal images. A simplified encryption technique is, first, presented using a single-fractal image and statistical analysis is performed. A general encryption system utilising multiple fractal images is, then, introduced to improve the performance and increase the encryption key up to hundreds of bits. This improvement is achieved through several parameters: feedback delay, multiplexing and independent horizontal or vertical shifts. The effect of each parameter is studied separately and, then, they are combined to illustrate their influence on the encryption quality. The encryption quality is evaluated using different analysis techniques such as correlation coefficients, differential attack measures, histogram distributions, key sensitivity analysis and the National Institute of Standards and Technology (NIST) statistical test suite. The obtained results show great potential compared to other techniques.

  13. 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. © 2014 ARVO.

  14. A High-Resolution Tile-Based Approach for Classifying Biological Regions in Whole-Slide Histopathological Images.

    Science.gov (United States)

    Hoffman, R A; Kothari, S; Phan, J H; Wang, M D

    Computational analysis of histopathological whole slide images (WSIs) has emerged as a potential means for improving cancer diagnosis and prognosis. However, an open issue relating to the automated processing of WSIs is the identification of biological regions such as tumor, stroma, and necrotic tissue on the slide. We develop a method for classifying WSI portions (512x512-pixel tiles) into biological regions by (1) extracting a set of 461 image features from each WSI tile, (2) optimizing tile-level prediction models using nested cross-validation on a small (600 tile) manually annotated tile-level training set, and (3) validating the models against a much larger (1.7x10 6 tile) data set for which ground truth was available on the whole-slide level. We calculated the predicted prevalence of each tissue region and compared this prevalence to the ground truth prevalence for each image in an independent validation set. Results show significant correlation between the predicted (using automated system) and reported biological region prevalences with p < 0.001 for eight of nine cases considered.

  15. Reliability demonstration of imaging surveillance systems

    International Nuclear Information System (INIS)

    Sheridan, T.F.; Henderson, J.T.; MacDiarmid, P.R.

    1979-01-01

    Security surveillance systems which employ closed circuit television are being deployed with increasing frequency for the protection of property and other valuable assets. A need exists to demonstrate the reliability of such systems before their installation to assure that the deployed systems will operate when needed with only the scheduled amount of maintenance and support costs. An approach to the reliability demonstration of imaging surveillance systems which employ closed circuit television is described. Failure definitions based on industry television standards and imaging alarm assessment criteria for surveillance systems are discussed. Test methods which allow 24 hour a day operation without the need for numerous test scenarios, test personnel and elaborate test facilities are presented. Existing reliability demonstration standards are shown to apply which obviate the need for elaborate statistical tests. The demonstration methods employed are shown to have applications in other types of imaging surveillance systems besides closed circuit television

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

    Science.gov (United States)

    Vargas, Hebert Alberto; Grimm, Jan; F Donati, Olivio; Sala, Evis; Hricak, Hedvig

    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. • Advanced imaging techniques allow direct visualisation of molecular interactions in prostate cancer. • MRI/PET, optical and Cerenkov imaging facilitate the translation of molecular biology. • Multiple compounds targeting PSMA expression are currently undergoing clinical translation. • Other targets (e.g., PSA, prostate-stem cell antigen, GRPR) are in development.

  17. Phase-contrast X-ray imaging using an X-ray interferometer for biological imaging

    Energy Technology Data Exchange (ETDEWEB)

    Momose, Atsushi; Koyama, Ichiro [Tokyo Univ., Dept. of Applied Physics, Tokyo (Japan); Takeda, Tohoru; Itai, Yuji [Tsukuba Univ., Inst. of Clinical Medicine, Tsukuba, Ibaraki (Japan); Yoneyama, Akio [Hitachi Ltd., Advanced Research Laboratory, Saitama (Japan)

    2002-04-01

    The potential of phase-contrast X-ray imaging using an X-ray interferometer is discussed comparing with other phase-contrast X-ray imaging methods, and its principle of contrast generation is presented including the case of phase-contrast X-ray computed tomography. The status of current instrumentation is described and perspectives for practical applications are discussed. (author)

  18. Breast imaging and reporting data system (BIRADS): Magnetic resonance imaging

    International Nuclear Information System (INIS)

    Tardivon, Anne A.; Athanasiou, Alexandra; Thibault, Fabienne; El Khoury, Carl

    2007-01-01

    This article reviews the technical aspects and interpretation criteria in breast MR imaging based on the first edition of breast imaging and reporting data system (BIRADS) published by the American College of Radiology (ACR) in 2003. In a second article, practical cases will be proposed for training the readers. The major aims of using this lexicon are: first to use a logical and standardized description of MR lesions, secondly to obtain a structured MR report with a clear final impression (BIRADS assessment categories), and thirdly to help comparison between different clinical studies based on similar breast MRI terminology

  19. Image quality in digital radiographic systems

    Directory of Open Access Journals (Sweden)

    Almeida Solange Maria de

    2003-01-01

    Full Text Available The aim of the present study was to evaluate the image quality of four direct digital radiographic systems. Radiographs were made of the maxillary central incisor and mandibular left molar regions of a dry skull, and an aluminum step-wedge. The X-ray generator operated at 10 mA, 60 and 70 kVp, and images were acquired with 3, 5, 8, 12, 24 and 48 exposure pulses. Six well-trained observers classified the images by means of scores from 1 to 3. Collected data were submitted to nonparametric statistical analysis using Fisher's exact test. Statistical analysis showed significant differences (p<0.01 in image quality with the four systems. Based on the results, it was possible to conclude that: 1 all of the digital systems presented good performance in producing acceptable images for diagnosis, if the exposures of the step-wedge and the maxillary central incisor region were made at 5 pulses, as well as at 8 pulses for the mandibular left molar region, selecting 60 or 70kVp; 2 higher percentages of acceptable images were obtained with the administration of lower radiation doses in CCD-sensors (charge-coupled device; 3 the Storage Phosphor systems produced acceptable images at a large range of exposure settings, that included low, intermediate and high radiation doses.

  20. Image acquisition system for traffic monitoring applications

    Science.gov (United States)

    Auty, Glen; Corke, Peter I.; Dunn, Paul; Jensen, Murray; Macintyre, Ian B.; Mills, Dennis C.; Nguyen, Hao; Simons, Ben

    1995-03-01

    An imaging system for monitoring traffic on multilane highways is discussed. The system, named Safe-T-Cam, is capable of operating 24 hours per day in all but extreme weather conditions and can capture still images of vehicles traveling up to 160 km/hr. Systems operating at different remote locations are networked to allow transmission of images and data to a control center. A remote site facility comprises a vehicle detection and classification module (VCDM), an image acquisition module (IAM) and a license plate recognition module (LPRM). The remote site is connected to the central site by an ISDN communications network. The remote site system is discussed in this paper. The VCDM consists of a video camera, a specialized exposure control unit to maintain consistent image characteristics, and a 'real-time' image processing system that processes 50 images per second. The VCDM can detect and classify vehicles (e.g. cars from trucks). The vehicle class is used to determine what data should be recorded. The VCDM uses a vehicle tracking technique to allow optimum triggering of the high resolution camera of the IAM. The IAM camera combines the features necessary to operate consistently in the harsh environment encountered when imaging a vehicle 'head-on' in both day and night conditions. The image clarity obtained is ideally suited for automatic location and recognition of the vehicle license plate. This paper discusses the camera geometry, sensor characteristics and the image processing methods which permit consistent vehicle segmentation from a cluttered background allowing object oriented pattern recognition to be used for vehicle classification. The image capture of high resolution images and the image characteristics required for the LPRMs automatic reading of vehicle license plates, is also discussed. The results of field tests presented demonstrate that the vision based Safe-T-Cam system, currently installed on open highways, is capable of producing automatic

  1. 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.

  2. International Conference on Intelligent Systems for Molecular Biology (ISMB)

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

    2009-12-29

    The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

  3. Request for Travel Funds for Systems Radiation Biology Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Barcellos-Hoff, Mary Helen [NYU School of Medicine

    2014-03-22

    The 3rd International Systems Radiation Biology Workshop brought together the major European, US and Japanese research programs on radiation risk as well as selected experts representing systems biological approaches to discuss how the new methodologies could be best exploited for low dose research. A significant part of the workshop was devoted to discussions organised as breakout group sessions. To facilitate discussions number of participants was limited to 60 persons. To achieve the goals of this symposium in this international conference, support from DOE is vital. Hence, this proposal requested support in the amount of $15,000 to cover the travel expenses of international experts and radiation biology scientists from the United States. This supporting mechanism was clearly identified to the selected US participants as a conference support award from the DOE (See attached PDF). The workshop was an outstanding opportunity to strengthen interactions between leading experts in the emerging areas of radiation sciences, and will also provide opportunities for younger scientists to meet with experts and discuss their results. This workshop was designed to endorse active engagement in international collaboration. A major objective of this conference was to effectively communicate research results, in order to ensure that current thinking reflects sound science of radiation biology. Further, this international event addressed the use and success of scientific initiatives in radiation biology for policymakers, standard-setters, and the general public.

  4. Hologlyphics: volumetric image synthesis performance system

    Science.gov (United States)

    Funk, Walter

    2008-02-01

    This paper describes a novel volumetric image synthesis system and artistic technique, which generate moving volumetric images in real-time, integrated with music. The system, called the Hologlyphic Funkalizer, is performance based, wherein the images and sound are controlled by a live performer, for the purposes of entertaining a live audience and creating a performance art form unique to volumetric and autostereoscopic images. While currently configured for a specific parallax barrier display, the Hologlyphic Funkalizer's architecture is completely adaptable to various volumetric and autostereoscopic display technologies. Sound is distributed through a multi-channel audio system; currently a quadraphonic speaker setup is implemented. The system controls volumetric image synthesis, production of music and spatial sound via acoustic analysis and human gestural control, using a dedicated control panel, motion sensors, and multiple musical keyboards. Music can be produced by external acoustic instruments, pre-recorded sounds or custom audio synthesis integrated with the volumetric image synthesis. Aspects of the sound can control the evolution of images and visa versa. Sounds can be associated and interact with images, for example voice synthesis can be combined with an animated volumetric mouth, where nuances of generated speech modulate the mouth's expressiveness. Different images can be sent to up to 4 separate displays. The system applies many novel volumetric special effects, and extends several film and video special effects into the volumetric realm. Extensive and various content has been developed and shown to live audiences by a live performer. Real world applications will be explored, with feedback on the human factors.

  5. Biological removal of algae in an integrated pond system

    CSIR Research Space (South Africa)

    Meiring, PGJ

    1995-01-01

    Full Text Available A system of oxidation ponds in series with a biological trickling filter is described. It was known that this arrangement was incapable of reducing effectively the levels of algae present in the pond liquid even though nitrification was effected...

  6. The role of analytical sciences in medical systems biology

    NARCIS (Netherlands)

    Greef, J. van der; Stroobant, P.; Heijden, R. van der

    2004-01-01

    Medical systems biology has generated widespread interest because of its bold conception and exciting potential, but the field is still in its infancy. Although there has been tremendous progress achieved recently in generating, integrating and analysing data in the medical and pharmaceutical field,

  7. Systems Biology for Mapping Genotype-Phenotype Relations in Yeast

    KAUST Repository

    Nielsen, Jens

    2016-01-01

    . Besides its wide industrial use, S. cerevisiae serves as an eukaryal model organism, and many systems biology tools have therefore been developed for this organism. Among these genome-scale metabolic models have shown to be most successful as they easy

  8. Separating intrinsic from extrinsic fluctuations in dynamic biological systems.

    Science.gov (United States)

    Hilfinger, Andreas; Paulsson, Johan

    2011-07-19

    From molecules in cells to organisms in ecosystems, biological populations fluctuate due to the intrinsic randomness of individual events and the extrinsic influence of changing environments. The combined effect is often too complex for effective analysis, and many studies therefore make simplifying assumptions, for example ignoring either intrinsic or extrinsic effects to reduce the number of model assumptions. Here we mathematically demonstrate how two identical and independent reporters embedded in a shared fluctuating environment can be used to identify intrinsic and extrinsic noise terms, but also how these contributions are qualitatively and quantitatively different from what has been previously reported. Furthermore, we show for which classes of biological systems the noise contributions identified by dual-reporter methods correspond to the noise contributions predicted by correct stochastic models of either intrinsic or extrinsic mechanisms. We find that for broad classes of systems, the extrinsic noise from the dual-reporter method can be rigorously analyzed using models that ignore intrinsic stochasticity. In contrast, the intrinsic noise can be rigorously analyzed using models that ignore extrinsic stochasticity only under very special conditions that rarely hold in biology. Testing whether the conditions are met is rarely possible and the dual-reporter method may thus produce flawed conclusions about the properties of the system, particularly about the intrinsic noise. Our results contribute toward establishing a rigorous framework to analyze dynamically fluctuating biological systems.

  9. CINRG: Systems Biology of Glucocorticoids in Muscle Disease

    Science.gov (United States)

    2013-10-01

    Contract W81XWH-09-1-0726 SYSTEMS BIOLOGY OF GLUCOCORTICOIDS IN MUSCLE DISEASE Introduction Duchenne muscular dystrophy (DMD) is the most... muscle and enable the development of better targeted and more effective therapies for Duchenne muscular dystrophy dynamically. This MDA grant...common and incurable muscular dystrophy of childhood. Muscle regeneration fails with advancing age, leading to considerable fibrosis. Corticosteroid

  10. System as metaphor in the psychology and biology of shame.

    Science.gov (United States)

    Maunder, R

    1996-01-01

    Biological theories of brain and psychological theories of mind are two systems of explanation that seem related to one another. The nature of the relationship is problematic and constitutes the age-old mind-body problem. The most prominent solutions currently are variations of materialism. While psychological theories can be consistent with materialism, there remains a difficulty in comprehending nonphysical (social, psychological) causes of physical effects. This difficulty is an obstacle to integration in psychiatry, where we routinely assume that illnesses that include or depend on biological dysfunction are caused multifactorially by causal agents such as perceived parental warmth, parental loss, stressful life events, genetics, and personality (Hammen et al. 1992; Kendler et al. 1993). Unity theory adopts the stance that neurobiological theories and psychological theories are essentially disparate explanations of the same psychobiological events; thus the relationship of mind to brain is one of shared reference (Goodman 1991; Maunder 1995). In Goodman's model the gap between biological and psychological systems is not bridgeable. Different conceptual categories refer to the same referents but cannot interact with each other. Stepping into the breach, systems theory has been presented as offering a language that can bridge the gap between psychological and biological theories of causation (Schwartz 1981; Weiner 1989). Thus, there is a controversy about the applicability of systems theory for integration in psychiatry.

  11. FIELD INVESTIGATION OF BIOLOGICAL TOILET SYSTEMS AND GREY WATER TREATMENT

    Science.gov (United States)

    The objective of the field program was to determine the operational characteristics and overall acceptability of popular models of biological toilets and a few select grey water systems. A field observation scheme was devised to take advantage of in-use sites throughout the State...

  12. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. Small programs as building unit. Why PERL? Why not BioPerl? Why not PERL modules? Advantage of independent programs. Language independent; Can be run independently.

  13. GPSR: A Resource for Genomics Proteomics and Systems Biology

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. GPSR: A Resource for Genomics Proteomics and Systems Biology. A journey from simple computer programs to drug/vaccine informatics. Limitations of existing web services. History repeats (Web to Standalone); Graphics vs command mode. General purpose ...

  14. Advances in reproductive biology and seed production systems of ...

    African Journals Online (AJOL)

    Eucalyptus globulus is the main eucalypt species grown in Australian plantations. The focus on seedling deployment systems, coupled with exploitation of large, open-pollinated base populations for breeding purposes over the last two decades, has required a detailed understanding of the reproductive biology of this ...

  15. Visual computing scientific visualization and imaging systems

    CERN Document Server

    2014-01-01

    This volume aims to stimulate discussions on research involving the use of data and digital images as an understanding approach for analysis and visualization of phenomena and experiments. The emphasis is put not only on graphically representing data as a way of increasing its visual analysis, but also on the imaging systems which contribute greatly to the comprehension of real cases. Scientific Visualization and Imaging Systems encompass multidisciplinary areas, with applications in many knowledge fields such as Engineering, Medicine, Material Science, Physics, Geology, Geographic Information Systems, among others. This book is a selection of 13 revised and extended research papers presented in the International Conference on Advanced Computational Engineering and Experimenting -ACE-X conferences 2010 (Paris), 2011 (Algarve), 2012 (Istanbul) and 2013 (Madrid). The examples were particularly chosen from materials research, medical applications, general concepts applied in simulations and image analysis and ot...

  16. Under sodium ultrasonic imaging system for PFBR

    International Nuclear Information System (INIS)

    Patankar, V.H.; Lalwani, S.K.; Agashe, A.A.

    2014-01-01

    Under Sodium UltraSonic Scanner (USUSS) has been developed to detect the growth and protrusion of fuel sub-assemblies of PFBR, submerged in liquid sodium by using the ultrasonic imaging technique during reactor shut-down when liquid sodium is at 180 ℃. The imaging is carried out prior to every Fuel handling operation. Electronics Division, BARC has designed and developed an 8-Channel Ultrasonic Imaging System (UIS) which consists of 4 downward viewing and 4 side viewing ultrasonic transducers alongwith pulser-receiver, signal processing electronics hardware and software. An automated mechanical scanner developed by IGCAR houses sodium immersible transducers to image the fuel sub assemblies. The system has been successfully tested with dummy protruding and grown FSAs, submerged under liquid sodium. Such ultrasonic imaging systems are not available to India from international market. The USUSS developed indigenously has all the features available in similar systems developed by other countries. After every imaging campaign, the mechanical scanner containing ultrasonic transducers is stored in the Argon filled storage-pit. Before every campaign of USUSS, it is necessary to check the healthiness of the sodium immersible and contaminated ultrasonic transducers, as the under-sodium scanner is decontaminated once in five years. For this purpose, a novel Non Contact Ultrasonic Inspection System (NCUIS) has been designed and developed by Electronics Division, BARC to check the functionality of the high-temperature and contaminated transducers of USUSS, using air-coupled ultrasonic technique. (author)

  17. Evaluation of transmitted images by teleradiology system

    International Nuclear Information System (INIS)

    Hoshikawa, Yoshikazu

    1993-01-01

    Teleradiology system is a combination of digital data networks and computer systems, which is the electric transmission of radiographs and/or radiologic images from local to center radiological system. The author evaluated reproducibility of transmitted images using Photophone (Image Data Corporation) as teleradiology system. Proven cases of abdominal free air (38 plain films, 15 CT), pneumothorax (24 plain films, 20 CT) and small bowel obstruction (30 plain films, 8 CT) were transmitted. Findings could be identified on non-magnified plain films in 75.6%, 83.3% and 96.7% respectively and on magnified CT in 100%, 100% and 100%. Transmitted images of 57 cases of abdominal trauma were read for positive findings and diagnosis by three radiologists. Average positive ratio was 47.3% on plain films and 70.9% on CT. Diagnosis was correct in 66.7% on CT. Specificity and sensitivity were 81.9% and 61.6% respectively on plain film and 88.6% and 93.9% on CT. The accuracy of transmitted images appears to be unsatisfactory on this study. It is suggested that the system is useful for consultation of already identified findings on the original images. (author)

  18. Evaluation of transmitted images by teleradiology system

    Energy Technology Data Exchange (ETDEWEB)

    Hoshikawa, Yoshikazu (St. Marianna Univ., Kawasaki (Japan). School of Medicine)

    1993-12-01

    Teleradiology system is a combination of digital data networks and computer systems, which is the electric transmission of radiographs and/or radiologic images from local to center radiological system. The author evaluated reproducibility of transmitted images using Photophone (Image Data Corporation) as teleradiology system. Proven cases of abdominal free air (38 plain films, 15 CT), pneumothorax (24 plain films, 20 CT) and small bowel obstruction (30 plain films, 8 CT) were transmitted. Findings could be identified on non-magnified plain films in 75.6%, 83.3% and 96.7% respectively and on magnified CT in 100%, 100% and 100%. Transmitted images of 57 cases of abdominal trauma were read for positive findings and diagnosis by three radiologists. Average positive ratio was 47.3% on plain films and 70.9% on CT. Diagnosis was correct in 66.7% on CT. Specificity and sensitivity were 81.9% and 61.6% respectively on plain film and 88.6% and 93.9% on CT. The accuracy of transmitted images appears to be unsatisfactory on this study. It is suggested that the system is useful for consultation of already identified findings on the original images. (author).

  19. EPR spectroscopy of complex biological iron-sulfur systems.

    Science.gov (United States)

    Hagen, Wilfred R

    2018-02-21

    From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.

  20. Applications of membrane computing in systems and synthetic biology

    CERN Document Server

    Gheorghe, Marian; Pérez-Jiménez, Mario

    2014-01-01

    Membrane Computing was introduced as a computational paradigm in Natural Computing. The models introduced, called Membrane (or P) Systems, provide a coherent platform to describe and study living cells as computational systems. Membrane Systems have been investigated for their computational aspects and employed to model problems in other fields, like: Computer Science, Linguistics, Biology, Economy, Computer Graphics, Robotics, etc. Their inherent parallelism, heterogeneity and intrinsic versatility allow them to model a broad range of processes and phenomena, being also an efficient means to solve and analyze problems in a novel way. Membrane Computing has been used to model biological systems, becoming with time a thorough modeling paradigm comparable, in its modeling and predicting capabilities, to more established models in this area. This book is the result of the need to collect, in an organic way, different facets of this paradigm. The chapters of this book, together with the web pages accompanying th...