WorldWideScience

Sample records for biological imaging system

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  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. 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

  18. 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

  19. 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)

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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."

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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...

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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...

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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 ...

  15. 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

  16. 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.

  17. 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).

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-17

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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. Integrated light-sheet imaging and flow-based enquiry (iLIFE) system for 3D in-vivo imaging of multicellular organism

    Science.gov (United States)

    Rasmi, Chelur K.; Padmanabhan, Sreedevi; Shirlekar, Kalyanee; Rajan, Kanhirodan; Manjithaya, Ravi; Singh, Varsha; Mondal, Partha Pratim

    2017-12-01

    We propose and demonstrate a light-sheet-based 3D interrogation system on a microfluidic platform for screening biological specimens during flow. To achieve this, a diffraction-limited light-sheet (with a large field-of-view) is employed to optically section the specimens flowing through the microfluidic channel. This necessitates optimization of the parameters for the illumination sub-system (illumination intensity, light-sheet width, and thickness), microfluidic specimen platform (channel-width and flow-rate), and detection sub-system (camera exposure time and frame rate). Once optimized, these parameters facilitate cross-sectional imaging and 3D reconstruction of biological specimens. The proposed integrated light-sheet imaging and flow-based enquiry (iLIFE) imaging technique enables single-shot sectional imaging of a range of specimens of varying dimensions, ranging from a single cell (HeLa cell) to a multicellular organism (C. elegans). 3D reconstruction of the entire C. elegans is achieved in real-time and with an exposure time of few hundred micro-seconds. A maximum likelihood technique is developed and optimized for the iLIFE imaging system. We observed an intracellular resolution for mitochondria-labeled HeLa cells, which demonstrates the dynamic resolution of the iLIFE system. The proposed technique is a step towards achieving flow-based 3D imaging. We expect potential applications in diverse fields such as structural biology and biophysics.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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)

  9. 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

  10. 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

  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. 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.

  13. 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.

  14. System for accessing a collection of histology images using content-based strategies

    International Nuclear Information System (INIS)

    Gonzalez F; Caicedo J C; Cruz Roa A; Camargo, J; Spinel, C

    2010-01-01

    Histology images are an important resource for research, education and medical practice. The availability of image collections with reference purposes is limited to printed formats such as books and specialized journals. When histology image sets are published in digital formats, they are composed of some tens of images that do not represent the wide diversity of biological structures that can be found in fundamental tissues; making a complete histology image collection available to the general public having a great impact on research and education in different areas such as medicine, biology and natural sciences. This work presents the acquisition process of a histology image collection with 20,000 samples in digital format, from tissue processing to digital image capturing. The main purpose of collecting these images is to make them available as reference material to the academic community. In addition, this paper presents the design and architecture of a system to query and explore the image collection, using content-based image retrieval tools and text-based search on the annotations provided by experts. The system also offers novel image visualization methods to allow easy identification of interesting images among hundreds of possible pictures. The system has been developed using a service-oriented architecture and allows web-based access in http://www.informed.unal.edu.co

  15. 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.

  16. 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.

  17. 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.

  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. 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. Advances of Molecular Imaging for Monitoring the Anatomical and Functional Architecture of the Olfactory System.

    Science.gov (United States)

    Zhang, Xintong; Bi, Anyao; Gao, Quansheng; Zhang, Shuai; Huang, Kunzhu; Liu, Zhiguo; Gao, Tang; Zeng, Wenbin

    2016-01-20

    The olfactory system of organisms serves as a genetically and anatomically model for studying how sensory input can be translated into behavior output. Some neurologic diseases are considered to be related to olfactory disturbance, especially Alzheimer's disease, Parkinson's disease, multiple sclerosis, and so forth. However, it is still unclear how the olfactory system affects disease generation processes and olfaction delivery processes. Molecular imaging, a modern multidisciplinary technology, can provide valid tools for the early detection and characterization of diseases, evaluation of treatment, and study of biological processes in living subjects, since molecular imaging applies specific molecular probes as a novel approach to produce special data to study biological processes in cellular and subcellular levels. Recently, molecular imaging plays a key role in studying the activation of olfactory system, thus it could help to prevent or delay some diseases. Herein, we present a comprehensive review on the research progress of the imaging probes for visualizing olfactory system, which is classified on different imaging modalities, including PET, MRI, and optical imaging. Additionally, the probes' design, sensing mechanism, and biological application are discussed. Finally, we provide an outlook for future studies in this field.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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...

  8. 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

  9. 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.

  10. 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)

  11. 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.

  12. 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.

  13. 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.

  14. 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...

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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.

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

    Science.gov (United States)

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

    2016-03-01

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

  1. 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....

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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)

  9. 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).

  10. 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.

  11. 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

  12. Towards native-state imaging in biological context in the electron microscope

    Science.gov (United States)

    Weston, Anne E.; Armer, Hannah E. J.

    2009-01-01

    Modern cell biology is reliant on light and fluorescence microscopy for analysis of cells, tissues and protein localisation. However, these powerful techniques are ultimately limited in resolution by the wavelength of light. Electron microscopes offer much greater resolution due to the shorter effective wavelength of electrons, allowing direct imaging of sub-cellular architecture. The harsh environment of the electron microscope chamber and the properties of the electron beam have led to complex chemical and mechanical preparation techniques, which distance biological samples from their native state and complicate data interpretation. Here we describe recent advances in sample preparation and instrumentation, which push the boundaries of high-resolution imaging. Cryopreparation, cryoelectron microscopy and environmental scanning electron microscopy strive to image samples in near native state. Advances in correlative microscopy and markers enable high-resolution localisation of proteins. Innovation in microscope design has pushed the boundaries of resolution to atomic scale, whilst automatic acquisition of high-resolution electron microscopy data through large volumes is finally able to place ultrastructure in biological context. PMID:19916039

  13. 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.

  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. 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

  16. 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...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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 ...

  2. 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.

  3. 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.

  4. 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.

  5. 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...

  6. 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)

  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. 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.

  9. 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

  10. 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.

  11. 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...

  12. 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...

  13. Challenges in the Design of Microwave Imaging Systems for Breast Cancer Detection

    DEFF Research Database (Denmark)

    Zhurbenko, Vitaliy

    2011-01-01

    community. This paper presents the survey of the ongoing research in the field of microwave imaging of biological tissues, with major focus on the breast tumor detection application. The existing microwave imaging systems are categorized on the basis of the employed measurement concepts. The advantages......Among the various breast imaging modalities for breast cancer detection, microwave imaging is attractive due to the high contrast in dielectric properties between the cancerous and normal tissue. Due to this reason, this modality has received a significant interest and attention from the microwave...... and disadvantages of the implemented imaging techniques are discussed. The fundamental tradeoffs between the various system requirements are indicated. Some strategies to overcome these limitations are outlined....

  14. 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.

  15. 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.

  16. 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),...

  17. 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.

  18. 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....

  19. Fiber laser-microscope system for femtosecond photodisruption of biological samples.

    Science.gov (United States)

    Yavaş, Seydi; Erdogan, Mutlu; Gürel, Kutan; Ilday, F Ömer; Eldeniz, Y Burak; Tazebay, Uygar H

    2012-03-01

    We report on the development of a ultrafast fiber laser-microscope system for femtosecond photodisruption of biological targets. A mode-locked Yb-fiber laser oscillator generates few-nJ pulses at 32.7 MHz repetition rate, amplified up to ∼125 nJ at 1030 nm. Following dechirping in a grating compressor, ∼240 fs-long pulses are delivered to the sample through a diffraction-limited microscope, which allows real-time imaging and control. The laser can generate arbitrary pulse patterns, formed by two acousto-optic modulators (AOM) controlled by a custom-developed field-programmable gate array (FPGA) controller. This capability opens the route to fine optimization of the ablation processes and management of thermal effects. Sample position, exposure time and imaging are all computerized. The capability of the system to perform femtosecond photodisruption is demonstrated through experiments on tissue and individual cells.

  20. 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.

  1. 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.

  2. 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.

  3. 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)

  4. 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)

  5. 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,...

  6. 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

  7. 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.

  8. A non-contact time-domain scanning brain imaging system: first in-vivo results

    Science.gov (United States)

    Mazurenka, M.; Di Sieno, L.; Boso, G.; Contini, D.; Pifferi, A.; Dalla Mora, A.; Tosi, A.; Wabnitz, H.; Macdonald, R.

    2013-06-01

    We present results of first in-vivo tests of an optical non-contact scanning imaging system, intended to study oxidative metabolism related processes in biological tissue by means of time-resolved near-infrared spectroscopy. Our method is a novel realization of the short source-detector separation approach and based on a fast-gated single-photon avalanche diode to detect late photons only. The scanning system is built in quasi-confocal configuration and utilizes polarizationsensitive detection. It scans an area of 4×4 cm2, recording images with 32×32 pixels, thus creating a high density of source-detector pairs. To test the system we performed a range of in vivo measurements of hemodynamic changes in several types of biological tissues, i.e. skin (Valsalva maneuver), muscle (venous and arterial occlusions) and brain (motor and cognitive tasks). Task-related changes in hemoglobin concentrations were clearly detected in skin and muscle. The brain activation shows weaker, but yet detectable changes. These changes were localized in pixels near the motor cortex area (C3). However, it was found that even very short hair substantially impairs the measurement. Thus the applicability of the scanner is limited to hairless parts of body. The results of our first in-vivo tests prove the feasibility of non-contact scanning imaging as a first step towards development of a prototype for biological tissue imaging for various medical applications.

  9. 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

  10. 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.

  11. Infrared laser transillumination CT imaging system using parallel fiber arrays and optical switches for finger joint imaging

    Science.gov (United States)

    Sasaki, Yoshiaki; Emori, Ryota; Inage, Hiroki; Goto, Masaki; Takahashi, Ryo; Yuasa, Tetsuya; Taniguchi, Hiroshi; Devaraj, Balasigamani; Akatsuka, Takao

    2004-05-01

    The heterodyne detection technique, on which the coherent detection imaging (CDI) method founds, can discriminate and select very weak, highly directional forward scattered, and coherence retaining photons that emerge from scattering media in spite of their complex and highly scattering nature. That property enables us to reconstruct tomographic images using the same reconstruction technique as that of X-Ray CT, i.e., the filtered backprojection method. Our group had so far developed a transillumination laser CT imaging method based on the CDI method in the visible and near-infrared regions and reconstruction from projections, and reported a variety of tomographic images both in vitro and in vivo of biological objects to demonstrate the effectiveness to biomedical use. Since the previous system was not optimized, it took several hours to obtain a single image. For a practical use, we developed a prototype CDI-based imaging system using parallel fiber array and optical switches to reduce the measurement time significantly. Here, we describe a prototype transillumination laser CT imaging system using fiber-optic based on optical heterodyne detection for early diagnosis of rheumatoid arthritis (RA), by demonstrating the tomographic imaging of acrylic phantom as well as the fundamental imaging properties. We expect that further refinements of the fiber-optic-based laser CT imaging system could lead to a novel and practical diagnostic tool for rheumatoid arthritis and other joint- and bone-related diseases in human finger.

  12. 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.

  13. Lateral resolution testing of a novel developed confocal microscopic imaging system

    Science.gov (United States)

    Zhang, Xin; Zhang, Yunhai; Chang, Jian; Huang, Wei; Xue, Xiaojun; Xiao, Yun

    2015-10-01

    Laser scanning confocal microscope has been widely used in biology, medicine and material science owing to its advantages of high resolution and tomographic imaging. Based on a set of confirmatory experiments and system design, a novel confocal microscopic imaging system is developed. The system is composed of a conventional fluorescence microscope and a confocal scanning unit. In the scanning unit a laser beam coupling module provides four different wavelengths 405nm 488nm 561nm and 638nm which can excite a variety of dyes. The system works in spot-to-spot scanning mode with a two-dimensional galvanometer. A 50 microns pinhole is used to guarantee that stray light is blocked and only the fluorescence signal from the focal point can be received . The three-channel spectral splitter is used to perform fluorescence imaging at three different working wavelengths simultaneously. The rat kidney tissue slice is imaged using the developed confocal microscopic imaging system. Nucleues labeled by DAPI and kidney spherule curved pipe labeled by Alexa Fluor 488 can be imaged clearly and respectively, realizing the distinction between the different components of mouse kidney tissue. The three-dimensional tomographic imaging of mouse kidney tissue is reconstructed by several two-dimensional images obtained in different depths. At last the resolution of the confocal microscopic imaging system is tested quantitatively. The experimental result shows that the system can achieve lateral resolution priority to 230nm.

  14. Flatbed-type 3D display systems using integral imaging method

    Science.gov (United States)

    Hirayama, Yuzo; Nagatani, Hiroyuki; Saishu, Tatsuo; Fukushima, Rieko; Taira, Kazuki

    2006-10-01

    We have developed prototypes of flatbed-type autostereoscopic display systems using one-dimensional integral imaging method. The integral imaging system reproduces light beams similar of those produced by a real object. Our display architecture is suitable for flatbed configurations because it has a large margin for viewing distance and angle and has continuous motion parallax. We have applied our technology to 15.4-inch displays. We realized horizontal resolution of 480 with 12 parallaxes due to adoption of mosaic pixel arrangement of the display panel. It allows viewers to see high quality autostereoscopic images. Viewing the display from angle allows the viewer to experience 3-D images that stand out several centimeters from the surface of the display. Mixed reality of virtual 3-D objects and real objects are also realized on a flatbed display. In seeking reproduction of natural 3-D images on the flatbed display, we developed proprietary software. The fast playback of the CG movie contents and real-time interaction are realized with the aid of a graphics card. Realization of the safety 3-D images to the human beings is very important. Therefore, we have measured the effects on the visual function and evaluated the biological effects. For example, the accommodation and convergence were measured at the same time. The various biological effects are also measured before and after the task of watching 3-D images. We have found that our displays show better results than those to a conventional stereoscopic display. The new technology opens up new areas of application for 3-D displays, including arcade games, e-learning, simulations of buildings and landscapes, and even 3-D menus in restaurants.

  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. 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)

  17. 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...

  18. 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...

  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. 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. 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....

  2. 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

  3. 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

  4. Miniature Compressive Ultra-spectral Imaging System Utilizing a Single Liquid Crystal Phase Retarder

    Science.gov (United States)

    August, Isaac; Oiknine, Yaniv; Abuleil, Marwan; Abdulhalim, Ibrahim; Stern, Adrian

    2016-03-01

    Spectroscopic imaging has been proved to be an effective tool for many applications in a variety of fields, such as biology, medicine, agriculture, remote sensing and industrial process inspection. However, due to the demand for high spectral and spatial resolution it became extremely challenging to design and implement such systems in a miniaturized and cost effective manner. Using a Compressive Sensing (CS) setup based on a single variable Liquid Crystal (LC) retarder and a sensor array, we present an innovative Miniature Ultra-Spectral Imaging (MUSI) system. The LC retarder acts as a compact wide band spectral modulator. Within the framework of CS, a sequence of spectrally modulated images is used to recover ultra-spectral image cubes. Using the presented compressive MUSI system, we demonstrate the reconstruction of gigapixel spatio-spectral image cubes from spectral scanning shots numbering an order of magnitude less than would be required using conventional systems.

  5. 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....

  6. 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.

  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. 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.

  9. 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...

  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. 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.

  12. 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.

  13. 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...

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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…

  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. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. Application of a new MR Microscope using an Independent Console System (MRMICS) for biological tissues in vitro

    International Nuclear Information System (INIS)

    Yoshioka, Hiroshi; Anno, Izumi; Itai, Yuji; Haishi, Tomoyuki; Adachi, Naotaka; Kose, Katsumi

    1999-01-01

    We studied microscopic MR images of the normal appendix in vitro using a new MR microscope system: MR Microscope using an Independent Console System (MRMICS). The MRMICS was placed in the clinical MR room, and the probe box was fixed on the bed of the 1.5 T clinical MR machine. T1-, T2-, and proton density-weighted images were obtained using spin echo sequences with an in-plane pixel size of 100 x 100 μm. Zonal structures of the appendix were clearly demonstrated with different contrast by different sequences. Therefore, the MRMICS is a useful add-on system for investigating microscopic MR images of biological tissues in vitro. (author)

  9. Application of a new MR Microscope using an Independent Console System (MRMICS) for biological tissues in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Yoshioka, Hiroshi; Anno, Izumi; Itai, Yuji [Tsukuba Univ., Ibaraki (Japan). Inst. of Clinical Medicine; Haishi, Tomoyuki; Adachi, Naotaka; Kose, Katsumi

    1999-02-01

    We studied microscopic MR images of the normal appendix in vitro using a new MR microscope system: MR Microscope using an Independent Console System (MRMICS). The MRMICS was placed in the clinical MR room, and the probe box was fixed on the bed of the 1.5 T clinical MR machine. T1-, T2-, and proton density-weighted images were obtained using spin echo sequences with an in-plane pixel size of 100 x 100 {mu}m. Zonal structures of the appendix were clearly demonstrated with different contrast by different sequences. Therefore, the MRMICS is a useful add-on system for investigating microscopic MR images of biological tissues in vitro. (author)

  10. Enhanced FIB-SEM systems for large-volume 3D imaging

    Science.gov (United States)

    Xu, C Shan; Hayworth, Kenneth J; Lu, Zhiyuan; Grob, Patricia; Hassan, Ahmed M; García-Cerdán, José G; Niyogi, Krishna K; Nogales, Eva; Weinberg, Richard J; Hess, Harald F

    2017-01-01

    Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 106 µm3. These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology. DOI: http://dx.doi.org/10.7554/eLife.25916.001 PMID:28500755

  11. 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.

  12. 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

  13. 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

  14. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    Energy Technology Data Exchange (ETDEWEB)

    Li, King C.P. [Department of Radiology, Methodist Hospital, Weill Cornell Medical College, 6565 Fannin Street, D280 Houston, TX 77030 (United States)], E-mail: kli@tmhs.org

    2009-05-15

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  15. From molecular imaging to systems diagnostics: Time for another paradigm shift?

    International Nuclear Information System (INIS)

    Li, King C.P.

    2009-01-01

    The term 'Molecular Imaging' has hit the consciousness of radiologists only in the past decade although many of the concepts that molecular imaging encompasses has been practiced in biomedical imaging, especially in nuclear medicine, for many decades. Many new imaging techniques have allowed us to interrogate biologic events at the cellular and molecular level in vivo in four dimensions but the challenge now is to translate these techniques into clinical practice in a way that will enable us to revolutionize healthcare delivery. The purpose of this article is to introduce the term 'Systems Diagnostics' and examine how radiologists can become translators of disparate sources of information into medical decisions and therapeutic actions.

  16. TL dosimetry for quality control of CR mammography imaging systems

    Science.gov (United States)

    Gaona, E.; Nieto, J. A.; Góngora, J. A. I. D.; Arreola, M.; Enríquez, J. G. F.

    The aim of this work is to estimate the average glandular dose with thermoluminescent (TL) dosimetry and comparison with quality imaging in computed radiography (CR) mammography. For a measuring dose, the Food and Drug Administration (FDA) and the American College of Radiology (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 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 flourohalideE 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 greater than 3.0 mGy without demonstrating improved image quality. 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 for X-rays with a HVL (0.35-0.38 mmAl) and kVp (24-26) used in quality control procedures with ACR Mammography Accreditation Phantom.

  17. 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.

  18. 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...

  19. 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.

  20. An automated robot arm system for small animal tissue biopsy under dual-image modality

    International Nuclear Information System (INIS)

    Huang, Y.H.; Wu, T.H.; Lin, M.H.; Yang, C.C.; Guo, W.Y.; Wang, Z.J.; Chen, C.L.; Lee, J.S.

    2006-01-01

    The ability to non-invasively monitor cell biology in vivo is one of the most important goals of molecular imaging. Imaging procedures could be inter-subject performed repeatedly at different investigating stages; thereby need not sacrifice small animals during the entire study period. Thus, the ultimate goal of this study was to design a stereotactic image-guided system for small animals and integrated it with an automatic robot arm for in vivo tissue biopsy analysis. The system was composed of three main parts, including one small animal stereotactic frame, one imaging-fusion software and an automatic robot arm system. The system has been thoroughly evaluated with three components; the robot position accuracy was 0.05±0.02 mm, the image registration accuracy was 0.37±0.18 mm and the system integration was satisfactorily within 1.20±0.39 mm of error. From these results, the system demonstrated sufficient accuracy to guide the micro-injector from the planned delivery routes into practice. The entire system accuracy was limited by the image fusion and orientation procedures, due to its nature of the blurred PET imaging obtained from the small objects. The primary improvement is to acquire as higher resolution as possible the fused imaging for localizing the targets in the future

  1. 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.

  2. Intravascular near-infrared fluorescence molecular imaging of atherosclerosis: toward coronary arterial visualization of biologically high-risk plaques

    Science.gov (United States)

    Calfon, Marcella A.; Vinegoni, Claudio; Ntziachristos, Vasilis; Jaffer, Farouc A.

    2010-01-01

    New imaging methods are urgently needed to identify high-risk atherosclerotic lesions prior to the onset of myocardial infarction, stroke, and ischemic limbs. Molecular imaging offers a new approach to visualize key biological features that characterize high-risk plaques associated with cardiovascular events. While substantial progress has been realized in clinical molecular imaging of plaques in larger arterial vessels (carotid, aorta, iliac), there remains a compelling, unmet need to develop molecular imaging strategies targeted to high-risk plaques in human coronary arteries. We present recent developments in intravascular near-IR fluorescence catheter-based strategies for in vivo detection of plaque inflammation in coronary-sized arteries. In particular, the biological, light transmission, imaging agent, and engineering principles that underlie a new intravascular near-IR fluorescence sensing method are discussed. Intravascular near-IR fluorescence catheters appear highly translatable to the cardiac catheterization laboratory, and thus may offer a new in vivo method to detect high-risk coronary plaques and to assess novel atherosclerosis biologics.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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...

  8. Controlled power delivery for super-resolution imaging of biological samples using digital micromirror device

    Science.gov (United States)

    Valiya Peedikakkal, Liyana; Cadby, Ashley

    2017-02-01

    Localization based super resolution images of a biological sample is generally achieved by using high power laser illumination with long exposure time which unfortunately increases photo-toxicity of a sample, making super resolution microscopy, in general, incompatible with live cell imaging. Furthermore, the limitation of photobleaching reduces the ability to acquire time lapse images of live biological cells using fluorescence microscopy. Digital Light Processing (DLP) technology can deliver light at grey scale levels by flickering digital micromirrors at around 290 Hz enabling highly controlled power delivery to samples. In this work, Digital Micromirror Device (DMD) is implemented in an inverse Schiefspiegler telescope setup to control the power and pattern of illumination for super resolution microscopy. We can achieve spatial and temporal patterning of illumination by controlling the DMD pixel by pixel. The DMD allows us to control the power and spatial extent of the laser illumination. We have used this to show that we can reduce the power delivered to the sample to allow for longer time imaging in one area while achieving sub-diffraction STORM imaging in another using higher power densities.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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)

  14. 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.

  15. 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

  16. 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.

  17. 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. ...

  18. 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.

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

    Science.gov (United States)

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

    2016-10-26

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

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

    Science.gov (United States)

    Nixon, Brenda Chaumont

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

  1. 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.

  2. 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...

  3. Discrimination methods for biological contaminants in fresh-cut lettuce based on VNIR and NIR hyperspectral imaging

    Science.gov (United States)

    Mo, Changyeun; Kim, Giyoung; Kim, Moon S.; Lim, Jongguk; Lee, Seung Hyun; Lee, Hong-Seok; Cho, Byoung-Kwan

    2017-09-01

    The rapid detection of biological contaminants such as worms in fresh-cut vegetables is necessary to improve the efficiency of visual inspections carried out by workers. Multispectral imaging algorithms were developed using visible-near-infrared (VNIR) and near-infrared (NIR) hyperspectral imaging (HSI) techniques to detect worms in fresh-cut lettuce. The optimal wavebands that can detect worms in fresh-cut lettuce were investigated for each type of HSI using one-way ANOVA. Worm-detection imaging algorithms for VNIR and NIR imaging exhibited prediction accuracies of 97.00% (RI547/945) and 100.0% (RI1064/1176, SI1064-1176, RSI-I(1064-1173)/1064, and RSI-II(1064-1176)/(1064+1176)), respectively. The two HSI techniques revealed that spectral images with a pixel size of 1 × 1 mm or 2 × 2 mm had the best classification accuracy for worms. The results demonstrate that hyperspectral reflectance imaging techniques have the potential to detect worms in fresh-cut lettuce. Future research relating to this work will focus on a real-time sorting system for lettuce that can simultaneously detect various defects such as browning, worms, and slugs.

  4. 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.

  5. 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.

  6. SeeStar: an open-source, low-cost imaging system for subsea observations

    Science.gov (United States)

    Cazenave, F.; Kecy, C. D.; Haddock, S.

    2016-02-01

    Scientists and engineers at the Monterey Bay Aquarium Research Institute (MBARI) have collaborated to develop SeeStar, a modular, light weight, self-contained, low-cost subsea imaging system for short- to long-term monitoring of marine ecosystems. SeeStar is composed of separate camera, battery, and LED lighting modules. Two versions of the system exist: one rated to 300 meters depth, the other rated to 1500 meters. Users can download plans and instructions from an online repository and build the system using low-cost off-the-shelf components. The system utilizes an easily programmable Arduino based controller, and the widely distributed GoPro camera. The system can be deployed in a variety of scenarios taking still images and video and can be operated either autonomously or tethered on a range of platforms, including ROVs, AUVs, landers, piers, and moorings. Several Seestar systems have been built and used for scientific studies and engineering tests. The long-term goal of this project is to have a widely distributed marine imaging network across thousands of locations, to develop baselines of biological information.

  7. 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.

  8. Nuclear medicine imaging instrumentations for molecular imaging

    International Nuclear Information System (INIS)

    Chung, Yong Hyun; Song, Tae Yong; Choi, Yong

    2004-01-01

    Small animal models are extensively utilized in the study of biomedical sciences. Current animal experiments and analysis are largely restricted to in vitro measurements and need to sacrifice animals to perform tissue or molecular analysis. This prevents researchers from observing in vivo the natural evolution of the process under study. Imaging techniques can provide repeatedly in vivo anatomic and molecular information noninvasively. Small animal imaging systems have been developed to assess biological process in experimental animals and increasingly employed in the field of molecular imaging studies. This review outlines the current developments in nuclear medicine imaging instrumentations including fused multi-modality imaging systems for small animal imaging

  9. Imaging system design and image interpolation based on CMOS image sensor

    Science.gov (United States)

    Li, Yu-feng; Liang, Fei; Guo, Rui

    2009-11-01

    An image acquisition system is introduced, which consists of a color CMOS image sensor (OV9620), SRAM (CY62148), CPLD (EPM7128AE) and DSP (TMS320VC5509A). The CPLD implements the logic and timing control to the system. SRAM stores the image data, and DSP controls the image acquisition system through the SCCB (Omni Vision Serial Camera Control Bus). The timing sequence of the CMOS image sensor OV9620 is analyzed. The imaging part and the high speed image data memory unit are designed. The hardware and software design of the image acquisition and processing system is given. CMOS digital cameras use color filter arrays to sample different spectral components, such as red, green, and blue. At the location of each pixel only one color sample is taken, and the other colors must be interpolated from neighboring samples. We use the edge-oriented adaptive interpolation algorithm for the edge pixels and bilinear interpolation algorithm for the non-edge pixels to improve the visual quality of the interpolated images. This method can get high processing speed, decrease the computational complexity, and effectively preserve the image edges.

  10. Hybrid system for in vivo real-time planar fluorescence and volumetric optoacoustic imaging

    Science.gov (United States)

    Chen, Zhenyue; Deán-Ben, Xosé Luís.; Gottschalk, Sven; Razansky, Daniel

    2018-02-01

    Fluorescence imaging is widely employed in all fields of cell and molecular biology due to its high sensitivity, high contrast and ease of implementation. However, the low spatial resolution and lack of depth information, especially in strongly-scattering samples, restrict its applicability for deep-tissue imaging applications. On the other hand, optoacoustic imaging is known to deliver a unique set of capabilities such as high spatial and temporal resolution in three dimensions, deep penetration and spectrally-enriched imaging contrast. Since fluorescent substances can generate contrast in both modalities, simultaneous fluorescence and optoacoustic readings can provide new capabilities for functional and molecular imaging of living organisms. Optoacoustic images can further serve as valuable anatomical references based on endogenous hemoglobin contrast. Herein, we propose a hybrid system for in vivo real-time planar fluorescence and volumetric optoacoustic tomography, both operating in reflection mode, which synergistically combines the advantages of stand-alone systems. Validation of the spatial resolution and sensitivity of the system were first carried out in tissue mimicking phantoms while in vivo imaging was further demonstrated by tracking perfusion of an optical contrast agent in a mouse brain in the hybrid imaging mode. Experimental results show that the proposed system effectively exploits the contrast mechanisms of both imaging modalities, making it especially useful for accurate monitoring of fluorescence-based signal dynamics in highly scattering samples.

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

    Science.gov (United States)

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

    2018-01-01

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

  12. [Development and applications of photosensitive device systems to biological studies]. Three year progress report

    International Nuclear Information System (INIS)

    1978-01-01

    The research has been directed to the two areas of x-ray diffraction and bioluminescence, with emphasis in the area of x-ray detection. Interest in x-ray image intensification techniques for biological and medical applications is long standing, and more and more utilized each year. During the past year, as the result of publications and participation in several workshops, the demonstrated advantages of our system over fast scan TV systems and multiwire chambers have become recognized, and several groups have requested us to supply them with a similar system. This is particularly true for use at the synchrotron x-ray sources. Although in recent years less effort has been spent in bioluminescence studies, results have been numerous, both in instrumentation development and experimental results. Bioluminescence is not only of interest in itself, but is a powerful tool for nondestructive study of other biological processes

  13. '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)

  14. 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.

  15. 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.

  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. 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...

  18. 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.

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

    Science.gov (United States)

    Ma, Qingyu; Gong, Xiufen; Zhang, Dong

    2006-12-22

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

  20. 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.

  1. 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’.

  2. BetaWB - A language for modular representation of biological systems

    DEFF Research Database (Denmark)

    Ihekwaba, Adoha; Larcher, Roberto; Mardare, Radu Iulian

    2007-01-01

    A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007......A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007...

  3. Measuring the Earth System in a Time of Global Environmental Change with Image Spectroscopy

    Science.gov (United States)

    Green, Robert O.

    2005-01-01

    Measuring the Earth system in a time of global environmental change. Imaging Spectroscopy enables remote measurement. Remote Measurement determination of the properties of the Earth's surface and atmosphere through the physics, chemistry and biology of the interaction of electromagnetic energy with matter.

  4. A Control System and Streaming DAQ Platform with Image-Based Trigger for X-ray Imaging

    Science.gov (United States)

    Stevanovic, Uros; Caselle, Michele; Cecilia, Angelica; Chilingaryan, Suren; Farago, Tomas; Gasilov, Sergey; Herth, Armin; Kopmann, Andreas; Vogelgesang, Matthias; Balzer, Matthias; Baumbach, Tilo; Weber, Marc

    2015-06-01

    High-speed X-ray imaging applications play a crucial role for non-destructive investigations of the dynamics in material science and biology. On-line data analysis is necessary for quality assurance and data-driven feedback, leading to a more efficient use of a beam time and increased data quality. In this article we present a smart camera platform with embedded Field Programmable Gate Array (FPGA) processing that is able to stream and process data continuously in real-time. The setup consists of a Complementary Metal-Oxide-Semiconductor (CMOS) sensor, an FPGA readout card, and a readout computer. It is seamlessly integrated in a new custom experiment control system called Concert that provides a more efficient way of operating a beamline by integrating device control, experiment process control, and data analysis. The potential of the embedded processing is demonstrated by implementing an image-based trigger. It records the temporal evolution of physical events with increased speed while maintaining the full field of view. The complete data acquisition system, with Concert and the smart camera platform was successfully integrated and used for fast X-ray imaging experiments at KIT's synchrotron radiation facility ANKA.

  5. Hyperspectral imaging flow cytometer

    Science.gov (United States)

    Sinclair, Michael B.; Jones, Howland D. T.

    2017-10-25

    A hyperspectral imaging flow cytometer can acquire high-resolution hyperspectral images of particles, such as biological cells, flowing through a microfluidic system. The hyperspectral imaging flow cytometer can provide detailed spatial maps of multiple emitting species, cell morphology information, and state of health. An optimized system can image about 20 cells per second. The hyperspectral imaging flow cytometer enables many thousands of cells to be characterized in a single session.

  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. 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.

  8. 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

  9. A dedicated database system for handling multi-level data in systems biology.

    Science.gov (United States)

    Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

    2014-01-01

    Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

  10. 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...

  11. 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

  12. 3D fingerprint imaging system based on full-field fringe projection profilometry

    Science.gov (United States)

    Huang, Shujun; Zhang, Zonghua; Zhao, Yan; Dai, Jie; Chen, Chao; Xu, Yongjia; Zhang, E.; Xie, Lili

    2014-01-01

    As an unique, unchangeable and easily acquired biometrics, fingerprint has been widely studied in academics and applied in many fields over the years. The traditional fingerprint recognition methods are based on the obtained 2D feature of fingerprint. However, fingerprint is a 3D biological characteristic. The mapping from 3D to 2D loses 1D information and causes nonlinear distortion of the captured fingerprint. Therefore, it is becoming more and more important to obtain 3D fingerprint information for recognition. In this paper, a novel 3D fingerprint imaging system is presented based on fringe projection technique to obtain 3D features and the corresponding color texture information. A series of color sinusoidal fringe patterns with optimum three-fringe numbers are projected onto a finger surface. From another viewpoint, the fringe patterns are deformed by the finger surface and captured by a CCD camera. 3D shape data of the finger can be obtained from the captured fringe pattern images. This paper studies the prototype of the 3D fingerprint imaging system, including principle of 3D fingerprint acquisition, hardware design of the 3D imaging system, 3D calibration of the system, and software development. Some experiments are carried out by acquiring several 3D fingerprint data. The experimental results demonstrate the feasibility of the proposed 3D fingerprint imaging system.

  13. 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

  14. 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.

  15. A New Multichannel Spectral Imaging Laser Scanning Confocal Microscope

    Directory of Open Access Journals (Sweden)

    Yunhai Zhang

    2013-01-01

    Full Text Available We have developed a new multichannel spectral imaging laser scanning confocal microscope for effective detection of multiple fluorescent labeling in the research of biological tissues. In this paper, the design and key technologies of the system are introduced. Representative results on confocal imaging, 3-dimensional sectioning imaging, and spectral imaging are demonstrated. The results indicated that the system is applicable to multiple fluorescent labeling in biological experiments.

  16. RGB color coded images in scanning electron microscopy of biological surfaces

    Czech Academy of Sciences Publication Activity Database

    Kofroňová, Olga; Benada, Oldřich

    2017-01-01

    Roč. 61, č. 3 (2017), s. 349-352 ISSN 0001-723X R&D Projects: GA MŠk(CZ) LO1509; GA ČR(CZ) GA16-20229S Institutional support: RVO:61388971 Keywords : Biological surfaces * Color image s * Scanning electron microscopy Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 0.673, year: 2016

  17. 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.

  18. 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...

  19. 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...

  20. 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.

  1. 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...

  2. 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.

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

    CSIR Research Space (South Africa)

    Mabaso, M

    2016-02-01

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

  4. 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.

  5. Unleashing elastic energy: dynamics of energy release in rubber bands and impulsive biological systems

    Science.gov (United States)

    Ilton, Mark; Cox, Suzanne; Egelmeers, Thijs; Patek, S. N.; Crosby, Alfred J.

    Impulsive biological systems - which include mantis shrimp, trap-jaw ants, and venus fly traps - can reach high speeds by using elastic elements to store and rapidly release energy. The material behavior and shape changes critical to achieving rapid energy release in these systems are largely unknown due to limitations of materials testing instruments operating at high speed and large displacement. In this work, we perform fundamental, proof-of-concept measurements on the tensile retraction of elastomers. Using high speed imaging, the kinematics of retraction are measured for elastomers with varying mechanical properties and geometry. Based on the kinematics, the rate of energy dissipation in the material is determined as a function of strain and strain-rate, along with a scaling relation which describes the dependence of maximum velocity on material properties. Understanding this scaling relation along with the material failure limits of the elastomer allows the prediction of material properties required for optimal performance. We demonstrate this concept experimentally by optimizing for maximum velocity in our synthetic model system, and achieve retraction velocities that exceed those in biological impulsive systems. This model system provides a foundation for future work connecting continuum performance to molecular architecture in impulsive systems.

  6. SU-G-IeP3-08: Image Reconstruction for Scanning Imaging System Based On Shape-Modulated Point Spreading Function

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruixing; Yang, LV [College of Optoelectronic Science and Engineering, National University of Defense Technology, Changsha, Hunan (China); Xu, Kele [College of Electronical Science and Engineering, National University of Defense Technology, Changsha, Hunan (China); Zhu, Li [Institute of Electrostatic and Electromagnetic Protection, Mechanical Engineering College, Shijiazhuang, Hebei (China)

    2016-06-15

    Purpose: Deconvolution is a widely used tool in the field of image reconstruction algorithm when the linear imaging system has been blurred by the imperfect system transfer function. However, due to the nature of Gaussian-liked distribution for point spread function (PSF), the components with coherent high frequency in the image are hard to restored in most of the previous scanning imaging system, even the relatively accurate PSF is acquired. We propose a novel method for deconvolution of images which are obtained by using shape-modulated PSF. Methods: We use two different types of PSF - Gaussian shape and donut shape - to convolute the original image in order to simulate the process of scanning imaging. By employing deconvolution of the two images with corresponding given priors, the image quality of the deblurred images are compared. Then we find the critical size of the donut shape compared with the Gaussian shape which has similar deconvolution results. Through calculation of tightened focusing process using radially polarized beam, such size of donut is achievable under same conditions. Results: The effects of different relative size of donut and Gaussian shapes are investigated. When the full width at half maximum (FWHM) ratio of donut and Gaussian shape is set about 1.83, similar resolution results are obtained through our deconvolution method. Decreasing the size of donut will favor the deconvolution method. A mask with both amplitude and phase modulation is used to create a donut-shaped PSF compared with the non-modulated Gaussian PSF. Donut with size smaller than our critical value is obtained. Conclusion: The utility of donutshaped PSF are proved useful and achievable in the imaging and deconvolution processing, which is expected to have potential practical applications in high resolution imaging for biological samples.

  7. 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…

  8. Special conference of the American Association for Cancer Research on molecular imaging in cancer: linking biology, function, and clinical applications in vivo.

    Science.gov (United States)

    Luker, Gary D

    2002-04-01

    The AACR Special Conference on Molecular Imaging in Cancer: Linking Biology, Function, and Clinical Applications In Vivo, was held January 23-27, 2002, at the Contemporary Hotel, Walt Disney World, Orlando, FL. Co-Chairs David Piwnica-Worms, Patricia Price and Thomas Meade brought together researchers with diverse expertise in molecular biology, gene therapy, chemistry, engineering, pharmacology, and imaging to accelerate progress in developing and applying technologies for imaging specific cellular and molecular signals in living animals and humans. The format of the conference was the presentation of research that focused on basic and translational biology of cancer and current state-of-the-art techniques for molecular imaging in animal models and humans. This report summarizes the special conference on molecular imaging, highlighting the interfaces of molecular biology with animal models, instrumentation, chemistry, and pharmacology that are essential to convert the dreams and promise of molecular imaging into improved understanding, diagnosis, and management of cancer.

  9. Stereoscopic Integrated Imaging Goggles for Multimodal Intraoperative Image Guidance.

    Directory of Open Access Journals (Sweden)

    Christopher A Mela

    Full Text Available We have developed novel stereoscopic wearable multimodal intraoperative imaging and display systems entitled Integrated Imaging Goggles for guiding surgeries. The prototype systems offer real time stereoscopic fluorescence imaging and color reflectance imaging capacity, along with in vivo handheld microscopy and ultrasound imaging. With the Integrated Imaging Goggle, both wide-field fluorescence imaging and in vivo microscopy are provided. The real time ultrasound images can also be presented in the goggle display. Furthermore, real time goggle-to-goggle stereoscopic video sharing is demonstrated, which can greatly facilitate telemedicine. In this paper, the prototype systems are described, characterized and tested in surgeries in biological tissues ex vivo. We have found that the system can detect fluorescent targets with as low as 60 nM indocyanine green and can resolve structures down to 0.25 mm with large FOV stereoscopic imaging. The system has successfully guided simulated cancer surgeries in chicken. The Integrated Imaging Goggle is novel in 4 aspects: it is (a the first wearable stereoscopic wide-field intraoperative fluorescence imaging and display system, (b the first wearable system offering both large FOV and microscopic imaging simultaneously,

  10. 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.

  11. 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

  12. 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)

  13. 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)

  14. 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.

  15. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems

    Science.gov (United States)

    Rellán-Álvarez, Rubén; Lobet, Guillaume; Lindner, Heike; Pradier, Pierre-Luc; Sebastian, Jose; Yee, Muh-Ching; Geng, Yu; Trontin, Charlotte; LaRue, Therese; Schrager-Lavelle, Amanda; Haney, Cara H; Nieu, Rita; Maloof, Julin; Vogel, John P; Dinneny, José R

    2015-01-01

    Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes. DOI: http://dx.doi.org/10.7554/eLife.07597.001 PMID:26287479

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. A global "imaging'' view on systems approaches in immunology.

    Science.gov (United States)

    Ludewig, Burkhard; Stein, Jens V; Sharpe, James; Cervantes-Barragan, Luisa; Thiel, Volker; Bocharov, Gennady

    2012-12-01

    The immune system exhibits an enormous complexity. High throughput methods such as the "-omic'' technologies generate vast amounts of data that facilitate dissection of immunological processes at ever finer resolution. Using high-resolution data-driven systems analysis, causal relationships between complex molecular processes and particular immunological phenotypes can be constructed. However, processes in tissues, organs, and the organism itself (so-called higher level processes) also control and regulate the molecular (lower level) processes. Reverse systems engineering approaches, which focus on the examination of the structure, dynamics and control of the immune system, can help to understand the construction principles of the immune system. Such integrative mechanistic models can properly describe, explain, and predict the behavior of the immune system in health and disease by combining both higher and lower level processes. Moving from molecular and cellular levels to a multiscale systems understanding requires the development of methodologies that integrate data from different biological levels into multiscale mechanistic models. In particular, 3D imaging techniques and 4D modeling of the spatiotemporal dynamics of immune processes within lymphoid tissues are central for such integrative approaches. Both dynamic and global organ imaging technologies will be instrumental in facilitating comprehensive multiscale systems immunology analyses as discussed in this review. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. 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.

  4. Systems biology for molecular life sciences and its impact in biomedicine.

    Science.gov (United States)

    Medina, Miguel Ángel

    2013-03-01

    Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

  5. 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 ‘‘...

  6. Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

    Science.gov (United States)

    De Domenico, Manlio

    2018-03-01

    Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

  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. 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.

  9. 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.

  10. 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 ...

  11. 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....

  12. 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.

  13. 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

  14. Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance.

    Science.gov (United States)

    Kalluri, Udaya C; Yin, Hengfu; Yang, Xiaohan; Davison, Brian H

    2014-12-01

    Fine-tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell wall and a high-precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high-resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis-expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high-precision tools for high-throughput assembly of multigene constructs and pathways, precision genome editing and site-specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems-level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  15. 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.

  16. THz near-field imaging of biological tissues employing synchrotron radiation

    International Nuclear Information System (INIS)

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

    2004-01-01

    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. 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.

  18. 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

  19. 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.

  20. 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...

  1. 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

  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. 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.

  4. 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.

  5. 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)

  6. Application of magnetic resonance imaging and spectroscopy in studying the biological effects of manufactured nanoparticles

    International Nuclear Information System (INIS)

    Lei Hao; Wei Li; Liu Maili

    2006-01-01

    With the rapid development of nanoscience and nanotechnology in recent years, growing research interest and efforts have been directed to study the biological effects of manufactured nanoparticles and substances alike. Despite the fact that significant progress has been made, this is still largely an uncharted field. Any advances in this field would certainly require thorough multi-disciplinary collaboration, in which the expertise and tools in nanoscience/nanotechnoloogy, physics, chemistry and biomedicine have to be combined. Due to their wide range of applications in physics, chemistry and biomedicine, magnetic resonance (MR) imaging and spectroscopy are among the most important and powerful research tools currently in use, mainly because these techniques can be used in situ and noninvasively to acquire dynamic and real-time information in various samples ranging from protein solution to the human brain. In this paper, the application of MR imaging and spectroscopy in studying the biological effects of manufactured nanoparticles is discussed. It is expected that these techniques will play important roles in 1) detecting the presence of nanoparticles in biological tissues and in vivo, 2) studying the interactions between the nanoparticles and biomolecules and 3) investigating the metabonomic aspect of the biological effects of nanoparticles. (authors)

  7. 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.

  8. 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

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

    Science.gov (United States)

    Garcia de Leon Valenzuela, Maria Julia

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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Suppression and enhancement of non-native molecules within biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Jones, E.A. [Surface Analysis Research Centre, CEAS, School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M60 1QD (United Kingdom)]. E-mail: e.jones@postgrad.manchester.ac.uk; Lockyer, N.P. [Surface Analysis Research Centre, CEAS, School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M60 1QD (United Kingdom); Vickerman, J.C. [Surface Analysis Research Centre, CEAS, School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M60 1QD (United Kingdom)

    2006-07-30

    With the aim of evaluating the potential of SIMS to provide molecular information from small molecules within biological systems, here we investigate the effect of different biological compounds as they act as matrices. The results highlight the fact that the chemical environment of a molecule can have a significant effect on its limit of detection. This has implications for the imaging of drugs and xenobiotics in tissue sections and other biological matrices. A 1:1 mixture of the organic acid 2,4,6-trihydroxyacetophenone and the dipeptide valine-valine demonstrates that almost complete suppression of the [M + H]{sup +} ion of one compound can be caused by the presence of a compound of higher proton affinity. The significance of this is highlighted when two similar drug molecules, atropine (a neutral molecule) and ipratropium bromide (a quaternary nitrogen containing salt) are mixed with brain homogenate. The atropine [M + H]{sup +} ion shows significant suppression whilst the [M - Br]{sup +} of ipratopium bromide is detected at an intensity that can be rationalised by its decreased surface concentration. By investigating the effect of two abundant tissue lipids, cholesterol and dipalmitoylphosphatidyl choline (DPPC), on the atropine [M + H]{sup +} signal detected in mixtures with these lipids we see that the DPPC has a strong suppressing effect, which may be attributed to gas phase proton transfer.

  15. Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S.; Fredrickson, J. K.; Stevens, R.

    2009-03-01

    Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

  16. Observation of dehydration dynamics in biological tissues with terahertz digital holography [Invited].

    Science.gov (United States)

    Guo, Lihan; Wang, Xinke; Han, Peng; Sun, Wenfeng; Feng, Shengfei; Ye, Jiasheng; Zhang, Yan

    2017-05-01

    A terahertz (THz) digital holographic imaging system is utilized to investigate natural dehydration processes in three types of biological tissues, including cattle, mutton, and pork. An image reconstruction algorithm is applied to remove the diffraction influence of THz waves and further improve clarity of THz images. From THz images of different biological specimens, distinctive water content as well as dehydration features of adipose and muscle tissues are precisely distinguished. By analyzing THz absorption spectra of these samples, temporal evolution characteristics of the absorbances for adipose and muscle tissues are described and compared in detail. Discrepancies between water retention ability of different animal tissues are also discussed. The imaging technique provides a valuable measurement platform for biological sensing.

  17. Hand-held hyperspectral imager for chemical/biological and environmental applications

    Science.gov (United States)

    Hinnrichs, Michele; Piatek, Bob

    2004-03-01

    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. 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

  19. 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

  20. 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.

  1. 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.

  2. 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).

  3. 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.

  4. 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.

  5. Palpation imaging using a haptic system for virtual reality applications in medicine.

    Science.gov (United States)

    Khaled, W; Reichling, S; Bruhns, O T; Boese, H; Baumann, M; Monkman, G; Egersdoerfer, S; Klein, D; Tunayar, A; Freimuth, H; Lorenz, A; Pessavento, A; Ermert, H

    2004-01-01

    In the field of medical diagnosis, there is a strong need to determine mechanical properties of biological tissue, which are of histological and pathological relevance. Malignant tumors are significantly stiffer than surrounding healthy tissue. One of the established diagnosis procedures is the palpation of body organs and tissue. Palpation is used to measure swelling, detect bone fracture, find and measure pulse, or to locate changes in the pathological state of tissue and organs. Current medical practice routinely uses sophisticated diagnostic tests through magnetic resonance imaging (MRI), computed tomography (CT) and ultrasound (US) imaging. However, they cannot provide direct measure of tissue elasticity. Last year we presented the concept of the first haptic sensor actuator system to visualize and reconstruct mechanical properties of tissue using ultrasonic elastography and a haptic display with electrorheological fluids. We developed a real time strain imaging system for tumor diagnosis. It allows biopsies simultaneously to conventional ultrasound B-Mode and strain imaging investigations. We deduce the relative mechanical properties by using finite element simulations and numerical solution models solving the inverse problem. Various modifications on the haptic sensor actuator system have been investigated. This haptic system has the potential of inducing real time substantial forces, using a compact lightweight mechanism which can be applied to numerous areas including intraoperative navigation, telemedicine, teaching and telecommunication.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. Flow measurements in biological systems using Xe-127 and Xe-133

    International Nuclear Information System (INIS)

    Tripathi, R.R.

    1981-01-01

    Xe-133 and Xe-127 are widely used for quantitative evaluation of ventilation in human subjects. Owing to differences in scattering in the biological system as well as differences in the detector response to photons of selected energies, clinical Xe-133 images are much more distorted than the corresponding Xe-127 images. This thesis concerns itself with the evaluation of Xe-133 and Xe-127 as potential tracers for pulmonary function studies. Through the simulation of clinical images it is shown that such smaller abnormalities are able to be detected with Xe-127 than with Xe-133. It is also found that even for poorly ventilated regions, the measured lesion size in the simulated image is comparable to the known lesion size when studied with Xe-127. With Xe-133, however, the measured size of the lesion is smaller than its known size. By fitting the washout portion of the clinical data to a linear sum of two exponentials, a weighted average clearance constant for the tracer - which relates to the reciprocal of the mean flow through the system - can be calculated and used as an index for comparison of the two Xenon isotopes. When an appropriate model is used for data interpretation, more accurate clinical information can be derived from the Xe-127 data. Unlike Xe-133, ventilation study with Xe-127 can be performed immediately after the perfusion study with Tc-99m. Lower radiation dose and longer shelf-life of Xe-127 are added advantages over Xe-133. Various compartmental and non-compartmental models are examined and appropriate technique(s) for clinical data interpretation is(are) recommended

  11. 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

  12. 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.

  13. Oligometastatic prostate cancer: shaping the definition with molecular imaging and an improved understanding of tumor biology.

    Science.gov (United States)

    Joice, Gregory A; Rowe, Steven P; Pienta, Kenneth J; Gorin, Michael A

    2017-11-01

    The aim of this review is to discuss how novel imaging modalities and molecular markers are shaping the definition of oligometastatic prostate cancer. To effectively classify a patient as having oligometastatic prostate cancer, diagnostic tests must be sensitive enough to detect subtle sites of metastatic disease. Conventional imaging modalities can readily detect widespread polymetastatic disease but do not have the sensitivity necessary to reliably classify patients as oligometastatic. Molecular imaging using both metabolic- and molecularly-targeted radiotracers has demonstrated great promise in aiding in our ability to define the oligometastatic state. Perhaps the most promising data to date have been generated with radiotracers targeting prostate-specific membrane antigen. In addition, early studies are beginning to define biologic markers in the oligometastatic state that may be indicative of disease with minimal metastatic potential. Recent developments in molecular imaging have allowed for improved detection of metastatic prostate cancer allowing for more accurate staging of patients with oligometastatic disease. Future development of biologic markers may assist in defining the oligometastatic state and determining prognosis.

  14. 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...

  15. The role of mechanics in biological and bio-inspired systems.

    Science.gov (United States)

    Egan, Paul; Sinko, Robert; LeDuc, Philip R; Keten, Sinan

    2015-07-06

    Natural systems frequently exploit intricate multiscale and multiphasic structures to achieve functionalities beyond those of man-made systems. Although understanding the chemical make-up of these systems is essential, the passive and active mechanics within biological systems are crucial when considering the many natural systems that achieve advanced properties, such as high strength-to-weight ratios and stimuli-responsive adaptability. Discovering how and why biological systems attain these desirable mechanical functionalities often reveals principles that inform new synthetic designs based on biological systems. Such approaches have traditionally found success in medical applications, and are now informing breakthroughs in diverse frontiers of science and engineering.

  16. 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

  17. A CMOS active pixel sensor system for laboratory- based x-ray diffraction studies of biological tissue

    International Nuclear Information System (INIS)

    Bohndiek, Sarah E; Cook, Emily J; Arvanitis, Costas D; Olivo, Alessandro; Royle, Gary J; Clark, Andy T; Prydderch, Mark L; Turchetta, Renato; Speller, Robert D

    2008-01-01

    X-ray diffraction studies give material-specific information about biological tissue. Ideally, a large area, low noise, wide dynamic range digital x-ray detector is required for laboratory-based x-ray diffraction studies. The goal of this work is to introduce a novel imaging technology, the CMOS active pixel sensor (APS) that has the potential to fulfil all these requirements, and demonstrate its feasibility for coherent scatter imaging. A prototype CMOS APS has been included in an x-ray diffraction demonstration system. An industrial x-ray source with appropriate beam filtration is used to perform angle dispersive x-ray diffraction (ADXRD). Optimization of the experimental set-up is detailed including collimator options and detector operating parameters. Scatter signatures are measured for 11 different materials, covering three medical applications: breast cancer diagnosis, kidney stone identification and bone mineral density calculations. Scatter signatures are also recorded for three mixed samples of known composition. Results are verified using two independent models for predicting the APS scatter signature: (1) a linear systems model of the APS and (2) a linear superposition integral combining known monochromatic scatter signatures with the input polychromatic spectrum used in this case. Cross validation of experimental, modelled and literature results proves that APS are able to record biologically relevant scatter signatures. Coherent scatter signatures are sensitive to multiple materials present in a sample and provide a means to quantify composition. In the future, production of a bespoke APS imager for x-ray diffraction studies could enable simultaneous collection of the transmitted beam and scattered radiation in a laboratory-based coherent scatter system, making clinical transfer of the technique attainable

  18. Heavy-ion microbeam system at JAEA-Takasaki for microbeam biology

    International Nuclear Information System (INIS)

    Funayama, Tomoo; Wada, Seiichi; Yokota, Yuichiro

    2008-01-01

    Research concerning cellular responses to low dose irradiation, radiation-induced bystander effects, and the biological track structure of charged particles has recently received particular attention in the field of radiation biology. Target irradiation employing a microbeam represents a useful means of advancing this research by obviating some of the disadvantages associated with the conventional irradiation strategies. The heavy-ion microbeam system at Japan Atomic Energy Agency (JAEA)-Takasaki, which was planned in 1987 and started in the early 1990's, can provide target irradiation of heavy charged particles to biological material at atmospheric pressure using a minimum beam size 5 μm in diameter. A variety of biological material has been irradiated using this microbeam system including cultured mammalian and higher plant cells, isolated fibers of mouse skeletal muscle, silkworm (Bombyx mori) embryos and larvae, Arabidopsis thaliana roots, and the nematode Caenorhabditis elegans. The system can be applied to the investigation of mechanisms within biological organisms not only in the context of radiation biology, but also in the fields of general biology such as physiology, developmental biology and neurobiology, and should help to establish and contribute to the field of 'microbeam biology'. (author)

  19. Holarchical Systems and Emotional Holons : Biologically-Inspired System Designs for Control of Autonomous Aerial Vehicles

    Science.gov (United States)

    Ippolito, Corey; Plice, Laura; Pisanich, Greg

    2003-01-01

    The BEES (Bio-inspired Engineering for Exploration Systems) for Mars project at NASA Ames Research Center has the goal of developing bio-inspired flight control strategies to enable aerial explorers for Mars scientific investigations. This paper presents a summary of our ongoing research into biologically inspired system designs for control of unmanned autonomous aerial vehicle communities for Mars exploration. First, we present cooperative design considerations for robotic explorers based on the holarchical nature of biological systems and communities. Second, an outline of an architecture for cognitive decision making and control of individual robotic explorers is presented, modeled after the emotional nervous system of cognitive biological systems. Keywords: Holarchy, Biologically Inspired, Emotional UAV Flight Control

  20. Computerized tomography using high resolution X-ray imaging system with a microfocus source

    International Nuclear Information System (INIS)

    Zaprazny, Z.; Korytar, D.; Konopka, P.; Ac, V.; Bielecki, J.

    2011-01-01

    In recent years there is an effort to image an internal structure of an object by using not only conventional 2D X-ray radiography but also using high resolution 3D tomography which is based on reconstruction of multiple 2D projections at various angular positions of the object. We have previously reported [1] the development and basic parameters of a high resolution x-ray imaging system with a microfocus source. We report the recent progress using this high resolution X-ray laboratory system in this work. These first findings show that our system is particularly suitable for light weight and nonmetallic objects such as biological objects, plastics, wood, paper, etc. where phase contrast helps to increase the visibility of the finest structures of the object. Phase-contrast X-ray Computerized Tomography is of our special interest because it is an emerging imaging technique that can be implemented at third generation synchrotron radiation sources and also in laboratory conditions using a microfocus X-ray tube or beam conditioning optics. (authors)

  1. Molecular imaging in biomedical research

    International Nuclear Information System (INIS)

    Jagannathan, N.R.

    2007-01-01

    Molecular imaging (MI) is a diverse technology that revolutionized preclinical, clinical and drug-discovery research. It integrates biology and medicine, and the technique presents a unique opportunity to examine living systems in vivo as a dynamic biological system. It is a hybrid technology that combines PET, SPECT, ultrasound, optical imaging and MR. Several MI methodologies are developed to examine the integrative functions of molecules, cells, organ systems and whole organisms. MI is superior to conventional diagnostic techniques in allowing better staging as well as to monitor the response of cancer/tumour to treatment. In addition, it helps visualization of specific molecular targets or pathways and cells in living systems and ultimately in the clinic. (author)

  2. 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

  3. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

    Directory of Open Access Journals (Sweden)

    Sorokin Anatoly

    2015-06-01

    Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

  4. 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....

  5. 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...

  6. 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

  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. 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...

  9. Predictive modelling of complex agronomic and biological systems.

    Science.gov (United States)

    Keurentjes, Joost J B; Molenaar, Jaap; Zwaan, Bas J

    2013-09-01

    Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead. © 2013 John Wiley & Sons Ltd.

  10. 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)

  11. 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.

  12. 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)

  13. 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.

  14. Quantitative computational models of molecular self-assembly in systems biology.

    Science.gov (United States)

    Thomas, Marcus; Schwartz, Russell

    2017-05-23

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  15. 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.

  16. Image acquisition and planimetry systems to develop wounding techniques in 3D wound model

    Directory of Open Access Journals (Sweden)

    Kiefer Ann-Kathrin

    2017-09-01

    Full Text Available Wound healing represents a complex biological repair process. Established 2D monolayers and wounding techniques investigate cell migration, but do not represent coordinated multi-cellular systems. We aim to use wound surface area measurements obtained from image acquisition and planimetry systems to establish our wounding technique and in vitro organotypic tissue. These systems will be used in our future wound healing treatment studies to assess the rate of wound closure in response to wound healing treatment with light therapy (photobiomodulation. The image acquisition and planimetry systems were developed, calibrated, and verified to measure wound surface area in vitro. The system consists of a recording system (Sony DSC HX60, 20.4 M Pixel, 1/2.3″ CMOS sensor and calibrated with 1mm scale paper. Macro photography with an optical zoom magnification of 2:1 achieves sufficient resolution to evaluate the 3mm wound size and healing growth. The camera system was leveled with an aluminum construction to ensure constant distance and orientation of the images. The JPG-format images were processed with a planimetry system in MATLAB. Edge detection enables definition of the wounded area. Wound area can be calculated with surface integrals. To separate the wounded area from the background, the image was filtered in several steps. Agar models, injured through several test persons with different levels of experience, were used as pilot data to test the planimetry software. These image acquisition and planimetry systems support the development of our wound healing research. The reproducibility of our wounding technique can be assessed by the variability in initial wound surface area. Also, wound healing treatment effects can be assessed by the change in rate of wound closure. These techniques represent the foundations of our wound model, wounding technique, and analysis systems in our ongoing studies in wound healing and therapy.

  17. Chemistry and biology of radiotracers that target changes in sympathetic and parasympathetic nervous systems in heart disease.

    Science.gov (United States)

    Eckelman, William C; Dilsizian, Vasken

    2015-06-01

    Following the discovery of the sympathetic and parasympathetic nervous system, numerous adrenoceptor drugs were radiolabeled and potent radioligands were prepared in order to image the β-adrenergic and the muscarinic systems. But the greatest effort has been in preparing noradrenaline analogs, such as norepinephrine, (11)C-metahydroxyephedrine, and (123)I-metaiodobenzylguanidine that measure cardiac sympathetic nerve varicosities. Given the technical and clinical challenges in designing and validating targeted adrenoceptor-binding radiotracers, namely the heavily weighted flow dependence and relatively low target-to-background ratio, both requiring complicated mathematic analysis, and the inability of targeted adrenoceptor radioligands to have an impact on clinical care of heart disease, the emphasis has been on radioligands monitoring the norepinephrine pathway. The chemistry and biology of such radiotracers, and the clinical and prognostic impact of these innervation imaging studies in patients with heart disease, are examined. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  18. Inverse Problems in Systems Biology: A Critical Review.

    Science.gov (United States)

    Guzzi, Rodolfo; Colombo, Teresa; Paci, Paola

    2018-01-01

    Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable. So the addition of a certain limited noise does not fundamentally change the situation but can be used to solve the so-called ill-posed problem, as defined by Hadamard. It can be seen as an extra source of information. Recent studies have shown that complex systems, among others the systems biology, are poorly constrained and ill-conditioned because it is difficult to use experimental data to fully estimate their parameters. For these reasons was born the concept of sloppy models, a sequence of models of increasing complexity that become sloppy in the limit of microscopic accuracy. Furthermore the concept of sloppy models contains also the concept of un-identifiability, because the models are characterized by many parameters that are poorly constrained by experimental data. Then a strategy needs to be designed to infer, analyze, and understand biological systems. The aim of this work is to provide a critical review to the inverse problems in systems biology defining a strategy to determine the minimal set of information needed to overcome the problems arising from dynamic biological models that generally may have many unknown, non-measurable parameters.

  19. Site-specific confocal fluorescence imaging of biological microstructures in a turbid medium

    International Nuclear Information System (INIS)

    Saloma, Caesar; Palmes-Saloma, Cynthia; Kondoh, Hisato

    1998-01-01

    Normally transparent biological structures in a turbid medium are imaged using a laser confocal microscope and multiwavelength site-specific fluorescence labelling. The spatial filtering capability of the detector pinhole in the confocal microscope limits the number of scattered fluorescent photons that reach the photodetector. Simultaneous application of different fluorescent markers on the same sample site minimizes photobleaching by reducing the excitation time for each marker. A high-contrast grey-level image is also produced by summing confocal images of the same site taken at different fluorescence wavelengths. Monte Carlo simulations are performed to obtain the quantitative behaviour of confocal fluorescence imaging in turbid media. Confocal images of the following samples were also obtained: (i) 15 μm diameter fluorescent spheres placed 1.16 mm deep beneath an aqueous suspension of 0.0823 μm diameter polystyrene latex spheres, and (ii) hindbrain of a whole-mount mouse embryo (age 10 days) that was stained to fluoresce at 515 nm and 580 nm peak wavelengths. Expression of RNA transcripts of a gene within the embryo hindbrain was detected by a fluorescence-based whole-mount in situ hybridization procedure that we recently tested. (author)

  20. 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.)

  1. 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.

  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. 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. PMID:22478806

  4. A dedicated database system for handling multi-level data in systems biology

    OpenAIRE

    Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

    2014-01-01

    Background Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging...

  5. 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

  6. [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.

  7. Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system.

    Science.gov (United States)

    Heppert, Jennifer K; Dickinson, Daniel J; Pani, Ariel M; Higgins, Christopher D; Steward, Annette; Ahringer, Julie; Kuhn, Jeffrey R; Goldstein, Bob

    2016-11-07

    Fluorescent protein tags are fundamental tools used to visualize gene products and analyze their dynamics in vivo. Recent advances in genome editing have expedited the precise insertion of fluorescent protein tags into the genomes of diverse organisms. These advances expand the potential of in vivo imaging experiments and facilitate experimentation with new, bright, photostable fluorescent proteins. Most quantitative comparisons of the brightness and photostability of different fluorescent proteins have been made in vitro, removed from biological variables that govern their performance in cells or organisms. To address the gap, we quantitatively assessed fluorescent protein properties in vivo in an animal model system. We generated transgenic Caenorhabditis elegans strains expressing green, yellow, or red fluorescent proteins in embryos and imaged embryos expressing different fluorescent proteins under the same conditions for direct comparison. We found that mNeonGreen was not as bright in vivo as predicted based on in vitro data but is a better tag than GFP for specific kinds of experiments, and we report on optimal red fluorescent proteins. These results identify ideal fluorescent proteins for imaging in vivo in C. elegans embryos and suggest good candidate fluorescent proteins to test in other animal model systems for in vivo imaging experiments. © 2016 Heppert et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  8. 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.

  9. Data publication with the structural biology data grid supports live analysis

    NARCIS (Netherlands)

    Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M J J|info:eu-repo/dai/nl/113691238; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung I.; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Fromme, J. Christopher; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercé; Sliz, Piotr

    2016-01-01

    Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology

  10. Advanced MR brain imaging. Why?

    International Nuclear Information System (INIS)

    Huisman, Thierry A.G.M.; Tekes, Aylin

    Repeated examinations, also known as so-called 'follow-up examinations' are nowadays frequently used to decide whether or not a chosen treatment should be continued, adapted or discontinued. The side effects of X-rays on biological systems, especially on developing systems did, however, limit the use of X-rays in children. The development of high-resolution, non-ionizing imaging modalities like US and MRI revolutionized diagnostic medicine for the second time after the discovery of X-rays. US is nowadays an essential imaging modality in paediatrics; it can be performed at the bedside, has no side effects on the child, is widely available, well accepted by parents and can be repeated without limitations. MRI with its high spatial resolution, different imaging contrasts and multiplanar capabilities has grown into a second line imaging modality if plain films and US cannot make the diagnosis accurately or reliably. A third revolution in diagnostic imaging occurred as MRI allowed studying biological processes and functions non-invasively. (orig.)

  11. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

    Science.gov (United States)

    Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  12. Systems Biology of Saccharomyces cerevisiae Physiology and its DNA Damage Response

    DEFF Research Database (Denmark)

    Fazio, Alessandro

    The yeast Saccharomyces cerevisiae is a model organism in biology, being widely used in fundamental research, the first eukaryotic organism to be fully sequenced and the platform for the development of many genomics techniques. Therefore, it is not surprising that S. cerevisiae has also been widely...... used in the field of systems biology during the last decade. This thesis investigates S. cerevisiae growth physiology and DNA damage response by using a systems biology approach. Elucidation of the relationship between growth rate and gene expression is important to understand the mechanisms regulating...... set of growth dependent genes by using a multi-factorial experimental design. Moreover, new insights into the metabolic response and transcriptional regulation of these genes have been provided by using systems biology tools (Chapter 3). One of the prerequisite of systems biology should...

  13. 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)

  14. Breast imaging with the SoftVue imaging system: first results

    Science.gov (United States)

    Duric, Neb; Littrup, Peter; Schmidt, Steven; Li, Cuiping; Roy, Olivier; Bey-Knight, Lisa; Janer, Roman; Kunz, Dave; Chen, Xiaoyang; Goll, Jeffrey; Wallen, Andrea; Zafar, Fouzaan; Allada, Veerendra; West, Erik; Jovanovic, Ivana; Li, Kuo; Greenway, William

    2013-03-01

    For women with dense breast tissue, who are at much higher risk for developing breast cancer, the performance of mammography is at its worst. Consequently, many early cancers go undetected when they are the most treatable. Improved cancer detection for women with dense breasts would decrease the proportion of breast cancers diagnosed at later stages, which would significantly lower the mortality rate. The emergence of whole breast ultrasound provides good performance for women with dense breast tissue, and may eliminate the current trade-off between the cost effectiveness of mammography and the imaging performance of more expensive systems such as magnetic resonance imaging. We report on the performance of SoftVue, a whole breast ultrasound imaging system, based on the principles of ultrasound tomography. SoftVue was developed by Delphinus Medical Technologies and builds on an early prototype developed at the Karmanos Cancer Institute. We present results from preliminary testing of the SoftVue system, performed both in the lab and in the clinic. These tests aimed to validate the expected improvements in image performance. Initial qualitative analyses showed major improvements in image quality, thereby validating the new imaging system design. Specifically, SoftVue's imaging performance was consistent across all breast density categories and had much better resolution and contrast. The implications of these results for clinical breast imaging are discussed and future work is described.

  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. Echinococcus as a model system: biology and epidemiology.

    Science.gov (United States)

    Thompson, R C A; Jenkins, D J

    2014-10-15

    The introduction of Echinococcus to Australia over 200 years ago and its establishment in sheep rearing areas of the country inflicted a serious medical and economic burden on the country. This resulted in an investment in both basic and applied research aimed at learning more about the biology and life cycle of Echinococcus. This research served to illustrate the uniqueness of the parasite in terms of developmental biology and ecology, and the value of Echinococcus as a model system in a broad range of research, from fundamental biology to theoretical control systems. These studies formed the foundation for an international, diverse and ongoing research effort on the hydatid organisms encompassing stem cell biology, gene regulation, strain variation, wildlife diseases and models of transmission dynamics. We describe the development, nature and diversity of this research, and how it was initiated in Australia but subsequently has stimulated much international and collaborative research on Echinococcus. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  17. 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.

  18. Chemical and biological studies on the technetium/S-unprotected MAG3-system

    International Nuclear Information System (INIS)

    Johannsen, B.; Noll, B.; Heise, K.H.; May, K.; Syhre, R.; Reiss, H.; Strangfeld, D.; Bruch, L.; Modersohn, D.

    1990-01-01

    Labelling studies performed with S-unprotected mercaptoacetylglycylglycine (MAG 3 ) have shown that various products of different biological properties exist in the Tc-MAG 3 system. Besides the known Tc(V)oxo complex recently introduced into nuclear medicine for renal function diagnosis, mainly three species were characterized by HPLC, TLC, electrophoresis and UV-VIS spectroscopy as well as biodistribution studies in rats and minipigs. Alteration of preparation conditions, both at carrier level (10 -4 M) and with no-carrier-added 99m Tc such as concentrations, sequence of reactants, pH, and time enabled to elucidate reaction routes within the system, interdependency of the Tc species, and vulnerability of the kidney imaging agent. The renal function agent was prepared by reduction of pertechnetate by stannous tartrate in solution of S-unprotected MAG 3 at pH > 11, and subsequent neutralization. (author)

  19. 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.

  20. 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...

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

    Science.gov (United States)

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

    2013-06-01

    Micro-computed tomography (micro-CT) is a high resolution imaging technique that has expanded and strengthened in use since it was last reviewed in this journal in 2004. The technology has expanded to include more detailed analysis of bone, as well as soft tissues, by use of various contrast agents. It is increasingly applied to questions in developmental biology and developmental toxicology. Relatively high-throughput protocols now provide a powerful and efficient means to evaluate embryos and fetuses subjected to genetic manipulations or chemical exposures. This review provides an overview of the technology, including scanning, reconstruction, visualization, segmentation, and analysis of micro-CT generated images. This is followed by a review of more recent applications of the technology in some common laboratory species that highlight the diverse issues that can be addressed. Copyright © 2013 Wiley Periodicals, Inc.

  2. 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)

  3. Intermediate Physics for Medicine and Biology

    CERN Document Server

    Hobbie, Russell K

    2007-01-01

    Intended for advanced undergraduate and beginning graduate students in biophysics, physiology, medical physics, cell biology, and biomedical engineering, this wide-ranging text bridges the gap between introductory physics and its application to the life and biomedical sciences. This extensively revised and updated fourth edition reflects new developments at the burgeoning interface between physics and biomedicine. Among the many topics treated are: forces in the skeletal system; fluid flow, with examples from the circulatory system; the logistic equation; scaling; transport of neutral particles by diffusion and by solvent drag; membranes and osmosis; equipartition of energy in statistical mechanics; the chemical potential and free energy; biological magnetic fields; membranes and gated channels in membranes; linear and nonlinear feedback systems; nonlinear phenomena, including biological clocks and chaotic behavior; signal analysis, noise and stochastic resonance detection of weak signals; image formation and...

  4. Graphene: One Material, Many Possibilities—Application Difficulties in Biological Systems

    Directory of Open Access Journals (Sweden)

    Marta Skoda

    2014-01-01

    Full Text Available Energetic technologies, nanoelectronics, biomedicine including gene therapy, cell imaging or tissue engineering are only few from all possible applications for graphene, the thinnest known carbon configuration and a basic element for other more complicated, better discovered and widely used nanostructures such as graphite, fullerenes and carbon nanotubes. The number of researches concerning graphene applications is rising every day which proves the great interest in its unique structure and properties. Ideal pristine graphene sheet presents a flat membrane of unlimited size with no imperfections while in practice we get different flakes with irregular edges and structural defects which influence the reactivity. Nanomaterials from graphene family differ in size, shape, layer number, lateral dimension, surface chemistry and defect density causing the existence of graphene samples with various influence on biological systems. Whether graphene induces cellular stress and activates apoptosis, or on the contrary facilitates growth and differentiation of the cells depends on its structure, chemical modifications and the growth process. A certain number of in vitro studies has indicated cytotoxic effects of graphene while the other show that it is safe. The diversity of the samples and methods of the production make it impossible to establish clearly the biological impact of graphene.

  5. Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases.

    Science.gov (United States)

    Oh, Soo Jin; Choi, Young Ki; Shin, Ok Sarah

    2018-03-01

    Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs. © Copyright: Yonsei University College of Medicine 2018.

  6. 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.

  7. 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

  8. 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.

  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. High resolution x-ray stereomicroscopy: True three-dimensional imaging of biological samples

    International Nuclear Information System (INIS)

    Loo, B.W.Jr.; Williams, S.; Meizel, S.; Rothman, S.S.; Univ. of California, Berkeley/San Francisco, CA; Univ. of California, San Francisco, CA

    1993-01-01

    X-ray microscopy has the potential to become a powerful tool for the study of biological samples, allowing the imaging of intact cells and subcellular organelles in an aqueous environment at resolutions previously achievable only by electron microscopy. The ability to examine a relatively thick sample raises the issue of superposition of objects from multiple planes within the sample, making difficult the interpretation of conventional, orthogonally projected images. This paper describes early attempts at developing three-dimensional methods for x-ray microimaging: the first to use x-ray optics, and to the authors' knowledge, the first demonstrating sub-visible resolutions and natural contrast. These studies were performed using the scanning transmission x-ray microscope (STXM) at the National Synchrotron Light Source, Brookhaven National Laboratory

  13. Assessing Biological Response to Bevacizumab Using 18F-Fluoromisonidazole PET/MR Imaging in a Patient with Recurrent Anaplastic Astrocytoma

    Directory of Open Access Journals (Sweden)

    Ramon F. Barajas

    2015-01-01

    Full Text Available We present our initial experience in using single modality fluoromisonidazole (FMISO PET/MR imaging to noninvasively evaluate the biological effects induced by bevacizumab therapy in a patient treated for recurrent high grade glioma. In this index patient, bevacizumab therapy resulted in the development of nonenhancing tumor characterized by reduced diffusion and markedly decreased FMISO uptake in the setting of maintained CBF and CBV. These observations suggest that the dynamic biological interplay between tissue hypoxia and vascular normalization occurring within treated recurrent high grade glioma can be captured utilizing FMISO PET/MR imaging.

  14. 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.

  15. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

    Directory of Open Access Journals (Sweden)

    Mi Huaiyu

    2015-06-01

    Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

  16. On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

    Science.gov (United States)

    Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

    2017-12-05

    The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

  17. 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. .

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

    Science.gov (United States)

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

    2013-10-01

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

  19. Stokes image reconstruction for two-color microgrid polarization imaging systems.

    Science.gov (United States)

    Lemaster, Daniel A

    2011-07-18

    The Air Force Research Laboratory has developed a new microgrid polarization imaging system capable of simultaneously reconstructing linear Stokes parameter images in two colors on a single focal plane array. In this paper, an effective method for extracting Stokes images is presented for this type of camera system. It is also shown that correlations between the color bands can be exploited to significantly increase overall spatial resolution. Test data is used to show the advantages of this approach over bilinear interpolation. The bounds (in terms of available reconstruction bandwidth) on image resolution are also provided.

  20. 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.

  1. 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)

  2. Photoacoustic contrast imaging of biological tissues with nanodiamonds fabricated for high near-infrared absorbance.

    Science.gov (United States)

    Zhang, Ti; Cui, Huizhong; Fang, Chia-Yi; Su, Long-Jyun; Ren, Shenqiang; Chang, Huan-Cheng; Yang, Xinmai; Forrest, M Laird

    2013-02-01

    Radiation-damaged nanodiamonds (DNDs) are potentially ideal optical contrast agents for photoacoustic (PA) imaging in biological tissues due to their low toxicity and high optical absorbance. PA imaging contrast agents have been limited to quantum dots and gold particles, since most existing carbon-based nanoparticles, including fluorescent nanodiamonds, do not have sufficient optical absorption in the near-infrared (NIR) range. A new DND by He+ ion beam irradiation with very high NIR absorption was synthesized. These DNDs produced a 71-fold higher PA signal on a molar basis than similarly dimensioned gold nanorods, and 7.1 fmol of DNDs injected into rodents could be clearly imaged 3 mm below the skin surface with PA signal enhancement of 567% using an 820-nm laser wavelength.

  3. Image registration for a UV-Visible dual-band imaging system

    Science.gov (United States)

    Chen, Tao; Yuan, Shuang; Li, Jianping; Xing, Sheng; Zhang, Honglong; Dong, Yuming; Chen, Liangpei; Liu, Peng; Jiao, Guohua

    2018-06-01

    The detection of corona discharge is an effective way for early fault diagnosis of power equipment. UV-Visible dual-band imaging can detect and locate corona discharge spot at all-weather condition. In this study, we introduce an image registration protocol for this dual-band imaging system. The protocol consists of UV image denoising and affine transformation model establishment. We report the algorithm details of UV image preprocessing, affine transformation model establishment and relevant experiments for verification of their feasibility. The denoising algorithm was based on a correlation operation between raw UV images, a continuous mask and the transformation model was established by using corner feature and a statistical method. Finally, an image fusion test was carried out to verify the accuracy of affine transformation model. It has proved the average position displacement error between corona discharge and equipment fault at different distances in a 2.5m-20 m range are 1.34 mm and 1.92 mm in the horizontal and vertical directions, respectively, which are precise enough for most industrial applications. The resultant protocol is not only expected to improve the efficiency and accuracy of such imaging system for locating corona discharge spot, but also supposed to provide a more generalized reference for the calibration of various dual-band imaging systems in practice.

  4. 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.

  5. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

    Directory of Open Access Journals (Sweden)

    Ina Aretz

    2016-04-01

    Full Text Available Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  6. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

    Science.gov (United States)

    Aretz, Ina; Meierhofer, David

    2016-04-27

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-01

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

  8. Specifications of Standards in Systems and Synthetic Biology.

    Science.gov (United States)

    Schreiber, Falk; Bader, Gary D; Golebiewski, Martin; Hucka, Michael; Kormeier, Benjamin; Le Novère, Nicolas; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar; Weise, Stephan

    2015-09-04

    Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation). Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/. So far the different standards were published and made accessible through the standards’ web- pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

  9. 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...

  10. Imaging differential polarization microscope with electronic readout

    International Nuclear Information System (INIS)

    Mickols, W.; Tinoco, I.; Katz, J.E.; Maestre, M.F.; Bustamante, C.

    1985-01-01

    A differential polarization microscope forms two images: one of the transmitted intensity and the other due to the change in intensity between images formed when different polarizations of light are used. The interpretation of these images for linear dichroism and circular dichroism are described. The design constraints on the data acquisition systems and the polarization modulation are described. The advantage of imaging several biological systems which contain optically anisotropic structures are described

  11. Deployment of a Fully-Automated Green Fluorescent Protein Imaging System in a High Arctic Autonomous Greenhouse

    Directory of Open Access Journals (Sweden)

    Alain Berinstain

    2013-03-01

    Full Text Available Higher plants are an integral part of strategies for sustained human presence in space. Space-based greenhouses have the potential to provide closed-loop recycling of oxygen, water and food. Plant monitoring systems with the capacity to remotely observe the condition of crops in real-time within these systems would permit operators to take immediate action to ensure optimum system yield and reliability. One such plant health monitoring technique involves the use of reporter genes driving fluorescent proteins as biological sensors of plant stress. In 2006 an initial prototype green fluorescent protein imager system was deployed at the Arthur Clarke Mars Greenhouse located in the Canadian High Arctic. This prototype demonstrated the advantageous of this biosensor technology and underscored the challenges in collecting and managing telemetric data from exigent environments. We present here the design and deployment of a second prototype imaging system deployed within and connected to the infrastructure of the Arthur Clarke Mars Greenhouse. This is the first imager to run autonomously for one year in the un-crewed greenhouse with command and control conducted through the greenhouse satellite control system. Images were saved locally in high resolution and sent telemetrically in low resolution. Imager hardware is described, including the custom designed LED growth light and fluorescent excitation light boards, filters, data acquisition and control system, and basic sensing and environmental control. Several critical lessons learned related to the hardware of small plant growth payloads are also elaborated.

  12. Deployment of a Fully-Automated Green Fluorescent Protein Imaging System in a High Arctic Autonomous Greenhouse

    Science.gov (United States)

    Abboud, Talal; Bamsey, Matthew; Paul, Anna-Lisa; Graham, Thomas; Braham, Stephen; Noumeir, Rita; Berinstain, Alain; Ferl, Robert

    2013-01-01

    Higher plants are an integral part of strategies for sustained human presence in space. Space-based greenhouses have the potential to provide closed-loop recycling of oxygen, water and food. Plant monitoring systems with the capacity to remotely observe the condition of crops in real-time within these systems would permit operators to take immediate action to ensure optimum system yield and reliability. One such plant health monitoring technique involves the use of reporter genes driving fluorescent proteins as biological sensors of plant stress. In 2006 an initial prototype green fluorescent protein imager system was deployed at the Arthur Clarke Mars Greenhouse located in the Canadian High Arctic. This prototype demonstrated the advantageous of this biosensor technology and underscored the challenges in collecting and managing telemetric data from exigent environments. We present here the design and deployment of a second prototype imaging system deployed within and connected to the infrastructure of the Arthur Clarke Mars Greenhouse. This is the first imager to run autonomously for one year in the un-crewed greenhouse with command and control conducted through the greenhouse satellite control system. Images were saved locally in high resolution and sent telemetrically in low resolution. Imager hardware is described, including the custom designed LED growth light and fluorescent excitation light boards, filters, data acquisition and control system, and basic sensing and environmental control. Several critical lessons learned related to the hardware of small plant growth payloads are also elaborated. PMID:23486220

  13. Evaluation of IsoCal geometric calibration system for Varian linacs equipped with on-board imager and electronic portal imaging device imaging systems.

    Science.gov (United States)

    Gao, Song; Du, Weiliang; Balter, Peter; Munro, Peter; Jeung, Andrew

    2014-05-08

    The purpose of this study is to evaluate the accuracy and reproducibility of the IsoCal geometric calibration system for kilovoltage (kV) and megavoltage (MV) imagers on Varian C-series linear accelerators (linacs). IsoCal calibration starts by imaging a phantom and collimator plate using MV images with different collimator angles, as well as MV and kV images at different gantry angles. The software then identifies objects on the collimator plate and in the phantom to determine the location of the treatment isocenter and its relation to the MV and kV imager centers. It calculates offsets between the positions of the imaging panels and the treatment isocenter as a function of gantry angle and writes a correction file that can be applied to MV and kV systems to correct for those offsets in the position of the panels. We performed IsoCal calibration three times on each of five Varian C-series linacs, each time with an independent setup. We then compared the IsoCal calibrations with a simplified Winston-Lutz (WL)-based system and with a Varian cubic phantom (VC)-based system. The maximum IsoCal corrections ranged from 0.7 mm to 1.5 mm for MV and 0.9 mm to 1.8 mm for kV imagers across the five linacs. The variations in the three calibrations for each linac were less than 0.2 mm. Without IsoCal correction, the WL results showed discrepancies between the treatment isocenter and the imager center of 0.9 mm to 1.6 mm (for the MV imager) and 0.5 mm to 1.1 mm (for the kV imager); with IsoCal corrections applied, the differences were reduced to 0.2 mm to 0.6 mm (MV) and 0.3 mm to 0.6 mm (kV) across the five linacs. The VC system was not as precise as the WL system, but showed similar results, with discrepancies of less than 1.0 mm when the IsoCal corrections were applied. We conclude that IsoCal is an accurate and consistent method for calibration and periodic quality assurance of MV and kV imaging systems.

  14. 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

  15. Quantitative, high-resolution proteomics for data-driven systems biology

    DEFF Research Database (Denmark)

    Cox, J.; Mann, M.

    2011-01-01

    Systems biology requires comprehensive data at all molecular levels. Mass spectrometry (MS)-based proteomics has emerged as a powerful and universal method for the global measurement of proteins. In the most widespread format, it uses liquid chromatography (LC) coupled to high-resolution tandem...... primary structure of proteins including posttranslational modifications, to localize proteins to organelles, and to determine protein interactions. Here, we describe the principles of analysis and the areas of biology where proteomics can make unique contributions. The large-scale nature of proteomics...... data and its high accuracy pose special opportunities as well as challenges in systems biology that have been largely untapped so far....

  16. 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

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Benjamin L. Franc

    2003-10-01

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

  19. 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)

  20. TECHNOLOGIES OF BRAIN IMAGES PROCESSING

    Directory of Open Access Journals (Sweden)

    O.M. Klyuchko

    2017-12-01

    Full Text Available The purpose of present research was to analyze modern methods of processing biological images implemented before storage in databases for biotechnological purposes. The databases further were incorporated into web-based digital systems. Examples of such information systems were described in the work for two levels of biological material organization; databases for storing data of histological analysis and of whole brain were described. Methods of neuroimaging processing for electronic brain atlas were considered. It was shown that certain pathological features can be revealed in histological image processing. Several medical diagnostic techniques (for certain brain pathologies, etc. as well as a few biotechnological methods are based on such effects. Algorithms of image processing were suggested. Electronic brain atlas was conveniently for professionals in different fields described in details. Approaches of brain atlas elaboration, “composite” scheme for large deformations as well as several methods of mathematic images processing were described as well.

  1. Magnetic resonance imaging. Recent studies on biological effects of static magnetic and high-frequency electromagnetic fields

    International Nuclear Information System (INIS)

    Pophof, B.; Brix, G.

    2017-01-01

    During the last few years, new studies on biological effects of strong static magnetic fields and on thermal effects of high-frequency electromagnetic fields used in magnetic resonance imaging (MRI) were published. Many of these studies have not yet been included in the current safety recommendations. Scientific publications since 2010 on biological effects of static and electromagnetic fields in MRI were researched and evaluated. New studies confirm older publications that have already described effects of static magnetic fields on sensory organs and the central nervous system, accompanied by sensory perceptions. A new result is the direct effect of Lorentz forces on ionic currents in the semicircular canals of the vestibular system. Recent studies of thermal effects of high-frequency electromagnetic fields were focused on the development of anatomically realistic body models and a more precise simulation of exposure scenarios. Strong static magnetic fields can cause unpleasant sensations, in particular, vertigo. In addition, they can influence the performance of the medical staff and thus potentially endanger the patient's safety. As a precaution, medical personnel should move slowly within the field gradient. High-frequency electromagnetic fields lead to an increase in the temperature of patients' tissues and organs. This should be considered especially in patients with restricted thermoregulation and in pregnant women and neonates; in these cases exposure should be kept as low as possible. (orig.) [de

  2. Use of a highly sensitive two-dimensional luminescence imaging system to monitor endogenous bioluminescence in plant leaves

    Directory of Open Access Journals (Sweden)

    Flor-Henry Michel

    2004-11-01

    Full Text Available Abstract Background All living organisms emit spontaneous low-level bioluminescence, which can be increased in response to stress. Methods for imaging this ultra-weak luminescence have previously been limited by the sensitivity of the detection systems used. Results We developed a novel configuration of a cooled charge-coupled device (CCD for 2-dimensional imaging of light emission from biological material. In this study, we imaged photon emission from plant leaves. The equipment allowed short integration times for image acquisition, providing high resolution spatial and temporal information on bioluminescence. We were able to carry out time course imaging of both delayed chlorophyll fluorescence from whole leaves, and of low level wound-induced luminescence that we showed to be localised to sites of tissue damage. We found that wound-induced luminescence was chlorophyll-dependent and was enhanced at higher temperatures. Conclusions The data gathered on plant bioluminescence illustrate that the equipment described here represents an improvement in 2-dimensional luminescence imaging technology. Using this system, we identify chlorophyll as the origin of wound-induced luminescence from leaves.

  3. Methodological challenges of optical tweezers-based X-ray fluorescence imaging of biological model organisms at synchrotron facilities.

    Science.gov (United States)

    Vergucht, Eva; Brans, Toon; Beunis, Filip; Garrevoet, Jan; Bauters, Stephen; De Rijcke, Maarten; Deruytter, David; Janssen, Colin; Riekel, Christian; Burghammer, Manfred; Vincze, Laszlo

    2015-07-01

    Recently, a radically new synchrotron radiation-based elemental imaging approach for the analysis of biological model organisms and single cells in their natural in vivo state was introduced. The methodology combines optical tweezers (OT) technology for non-contact laser-based sample manipulation with synchrotron radiation confocal X-ray fluorescence (XRF) microimaging for the first time at ESRF-ID13. The optical manipulation possibilities and limitations of biological model organisms, the OT setup developments for XRF imaging and the confocal XRF-related challenges are reported. In general, the applicability of the OT-based setup is extended with the aim of introducing the OT XRF methodology in all research fields where highly sensitive in vivo multi-elemental analysis is of relevance at the (sub)micrometre spatial resolution level.

  4. 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.

  5. 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.

  6. Tritium fractionation in biological systems and in analytical procedures

    International Nuclear Information System (INIS)

    Kim, M.A.; Baumgaertner, F.

    1991-01-01

    The organically bound tritium (OBT) is evaluated in biological systems by measuring the tritium distribution ratio (R-value), i.e. tritium concentrations in organic substance to tissue water. The determination of the R-value is found to involve always isotope fractionation in 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 fraction in the tissue 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 water systems as well as in real biological systems, e.g. maize plant. The results are systematically analysed and the influence of isotope effects on the R-value is rigorously quantified. (orig.)

  7. THz near-field imaging of biological tissues employing synchrotron radiation (Invited Paper)

    Science.gov (United States)

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

    2005-04-01

    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 on to the intrinsic time structure of the synchrotron radiation. The scanning microscope utilizes conical waveguides 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 λ/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 μm at about 12 wavenumbers (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 0.06 and 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.

  8. Fully Automated On-Chip Imaging Flow Cytometry System with Disposable Contamination-Free Plastic Re-Cultivation Chip

    Directory of Open Access Journals (Sweden)

    Tomoyuki Kaneko

    2011-06-01

    Full Text Available We have developed a novel imaging cytometry system using a poly(methyl methacrylate (PMMA based microfluidic chip. The system was contamination-free, because sample suspensions contacted only with a flammable PMMA chip and no other component of the system. The transparency and low-fluorescence of PMMA was suitable for microscopic imaging of cells flowing through microchannels on the chip. Sample particles flowing through microchannels on the chip were discriminated by an image-recognition unit with a high-speed camera in real time at the rate of 200 event/s, e.g., microparticles 2.5 μm and 3.0 μm in diameter were differentiated with an error rate of less than 2%. Desired cells were separated automatically from other cells by electrophoretic or dielectrophoretic force one by one with a separation efficiency of 90%. Cells in suspension with fluorescent dye were separated using the same kind of microfluidic chip. Sample of 5 μL with 1 × 106 particle/mL was processed within 40 min. Separated cells could be cultured on the microfluidic chip without contamination. The whole operation of sample handling was automated using 3D micropipetting system. These results showed that the novel imaging flow cytometry system is practically applicable for biological research and clinical diagnostics.

  9. 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.)

  10. Single-molecule imaging and manipulation of biomolecular machines and systems.

    Science.gov (United States)

    Iino, Ryota; Iida, Tatsuya; Nakamura, Akihiko; Saita, Ei-Ichiro; You, Huijuan; Sako, Yasushi

    2018-02-01

    Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Super-resolution and super-localization microscopy: A novel tool for imaging chemical and biological processes

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Bin [Iowa State Univ., Ames, IA (United States)

    2015-01-01

    Optical microscopy imaging of single molecules and single particles is an essential method for studying fundamental biological and chemical processes at the molecular and nanometer scale. The best spatial resolution (~ λ/2) achievable in traditional optical microscopy is governed by the diffraction of light. However, single molecule-based super-localization and super-resolution microscopy imaging techniques have emerged in the past decade. Individual molecules can be localized with nanometer scale accuracy and precision for studying of biological and chemical processes.This work uncovered the heterogeneous properties of the pore structures. In this dissertation, the coupling of molecular transport and catalytic reaction at the single molecule and single particle level in multilayer mesoporous nanocatalysts was elucidated. Most previous studies dealt with these two important phenomena separately. A fluorogenic oxidation reaction of non-fluorescent amplex red to highly fluorescent resorufin was tested. The diffusion behavior of single resorufin molecules in aligned nanopores was studied using total internal reflection fluorescence microscopy (TIRFM).

  12. 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.

  13. 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

  14. Biological Studies with Laser-Polarized ^129Xe

    Science.gov (United States)

    Tseng, C. H.; Oteiza, E. R.; Wong, G. A.; Walsworth, R. L.; Albert, M. S.; Nascimben, L.; Peled, S.; Sakai, K.; Jolesz, F. A.

    1996-05-01

    We have studied several biological systems using laser-polarized ^129Xe. In certain tissues magnetic resonance imaging (MRI) using inhaled laser-polarized noble gases may provide images superior to those from conventional proton MRI. High resolution laser-polarized ^3He images of air spaces in the human lung were recently obtained by the Princeton/Duke group. However, ^3He is not very soluble in tissue. Therefore, we are using laser polarized ^129Xe (tissue-soluble), with the long term goal of biomedical functional imaging. We have investigated multi-echo and multi-excitation magnetic resonance detection schemes to exploit the highly non-thermal ^129Xe magnetization produced by the laser polarization technique. We have inhalated live rats with laser-polarized ^129Xe gas and measured three distinct ^129Xe tissue resonances that last 20 to 40 sec. As a demonstration, we obtained a laser polarized ^129Xe image of the human oral cavity. Currently we are measuring the polarization lifetime of ^129Xe dissolved in human blood, the biological transporting medium. These studies and other recent developments will be reported.

  15. 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.

  16. 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.

  17. Method and apparatus for imaging substances in biological samples by nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Shaw, D.

    1984-01-01

    A method of determining the distribution of non-proton nuclei having a magnetic moment in a biological sample is described. It comprises subjecting the sample to a magnetic field, irradiating the sample with RF radiation at a proton magnetic resonance frequency and deriving a first NMR signal, indicative of electromagnetic absorption of the sample at the proton magnetic resonance frequency. A second such NMR signal at the proton resonance frequency is then derived from the sample in the presence of RF radiation at the nuclear magnetic resonance frequency of the non-proton nuclei so as to decouple protons in the sample from the non-proton nuclei. By applying an imaging technique, an image indicative of the spatial variation of the difference between the first and second signals can be produced. Imaging may be performed on the difference between the two NMR signals, or on each NMR signal followed by subtraction of the images. The method can be used to trace how a 13 C-labelled material introduced into a patient, and its breakdown products, become distributed. (author)

  18. The image acquisition system design of floor grinder

    Science.gov (United States)

    Wang, Yang-jiang; Liu, Wei; Liu, Hui-qin

    2018-01-01

    Based on linear CCD, high resolution image real-time acquisition system serves as designing a set of image acquisition system for floor grinder through the calculation of optical imaging system. The entire image acquisition system can collect images of ground before and after the work of the floor grinder, and the data is transmitted through the Bluetooth system to the computer and compared to realize real-time monitoring of its working condition. The system provides technical support for the design of unmanned ground grinders.

  19. 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.

  20. Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology

    KAUST Repository

    Gomez-Cabrero, David

    2017-08-23

    Summary Systems medicine and systems biology have inherent educational challenges. These have largely been addressed either by providing new masters programs or by redesigning undergraduate programs. In contrast, short courses can respond to a different need: they can provide condensed updates for professionals across academia, the clinic, and industry. These courses have received less attention. Here, we share our experiences in developing and providing such courses to current and future leaders in systems biology and systems medicine. We present guidelines for how to reproduce our courses, and we offer suggestions for how to select students who will nurture an interdisciplinary learning environment and thrive there.

  1. Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology

    KAUST Repository

    Gomez-Cabrero, David; Marabita, Francesco; Tarazona, Sonia; Cano, Isaac; Roca, Josep; Conesa, Ana; Sabatier, Philippe; Tegner, Jesper

    2017-01-01

    Summary Systems medicine and systems biology have inherent educational challenges. These have largely been addressed either by providing new masters programs or by redesigning undergraduate programs. In contrast, short courses can respond to a different need: they can provide condensed updates for professionals across academia, the clinic, and industry. These courses have received less attention. Here, we share our experiences in developing and providing such courses to current and future leaders in systems biology and systems medicine. We present guidelines for how to reproduce our courses, and we offer suggestions for how to select students who will nurture an interdisciplinary learning environment and thrive there.

  2. Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

    NARCIS (Netherlands)

    Cvijovic, Marija; Höfer, Thomas; Acimovic, Jure; Alberghina, Lilia; Almaas, Eivind; Besozzi, Daniela; Blomberg, Anders; Bretschneider, Till; Cascante, Marta; Collin, Olivier; Atauri, de Pedro; Depner, Cornelia; Dickinson, Robert; Dobrzynski, Maciej; Fleck, C.; Garcia-Ojalvo, Jordi; Gonze, Didier; Hahn, Jens; Hess, Heide Marie; Hollmann, Susanne; Krantz, Marcus; Kummer, Ursula; Lundh, Torbjörn; Martial, Gifta; Martins dos Santos, V.A.P.; Mauer-Oberthür, Angela; Regierer, Babette; Skene, Barbara; Stalidzans, Egils; Stelling, Jörg; Teusink, Bas; Workman, Christopher T.; Hohmann, Stefan

    2016-01-01

    Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological

  3. Functional mesoporous silica nanoparticles for bio-imaging applications.

    Science.gov (United States)

    Cha, Bong Geun; Kim, Jaeyun

    2018-03-22

    Biomedical investigations using mesoporous silica nanoparticles (MSNs) have received significant attention because of their unique properties including controllable mesoporous structure, high specific surface area, large pore volume, and tunable particle size. These unique features make MSNs suitable for simultaneous diagnosis and therapy with unique advantages to encapsulate and load a variety of therapeutic agents, deliver these agents to the desired location, and release the drugs in a controlled manner. Among various clinical areas, nanomaterials-based bio-imaging techniques have advanced rapidly with the development of diverse functional nanoparticles. Due to the unique features of MSNs, an imaging agent supported by MSNs can be a promising system for developing targeted bio-imaging contrast agents with high structural stability and enhanced functionality that enable imaging of various modalities. Here, we review the recent achievements on the development of functional MSNs for bio-imaging applications, including optical imaging, magnetic resonance imaging (MRI), positron emission tomography (PET), computed tomography (CT), ultrasound imaging, and multimodal imaging for early diagnosis. With further improvement in noninvasive bio-imaging techniques, the MSN-supported imaging agent systems are expected to contribute to clinical applications in the future. This article is categorized under: Diagnostic Tools > In vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology. © 2018 Wiley Periodicals, Inc.

  4. 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....

  5. 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...

  6. 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.

  7. 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

  8. Automatic detection of biological cells

    International Nuclear Information System (INIS)

    Alves Da Costa, Caiuby

    1983-01-01

    The present research work has dealt with the analysis of biological cell images in general, and more specially with the cervical cells. This work was carried out in order to develop an automaton leading to a better prevention of cancer through automated mass screening. The device has been implemented on Motorola 68.000 microprocessor system. The automaton carries out cell nucleus analysis in several steps. The main steps are: - First: the automaton focuses on an individual cell nucleus among the smear's cell (about 10.000), - Second: it process each nucleus image. The digital processing yields geometrical of the nucleus (area and perimeter) for each cell. These data are stored in a local memory for further discriminant analysis by a microcomputer. In this way smears are classed in two groups: hale smears and uncertain smears. The automaton uses a wired logic for image acquisition and its software algorithms provide image reconstruction. The reconstruction algorithms are general purpose. Tests have proved that they can reconstruct any two dimensional images independently of its geometrical form. Moreover they can make the reconstruction of any image among the several images present in observation field. The processing times registered during the tests (for different cases) were situated, all of them, below three minutes for 10,000 images (each of them formed by an average of 450 pixels). The interest of the method is generality and speed. The only restriction is the primary device sensor (CCD linear array) length. Thus the automaton application can be extended beyond the biological image field. (author) [fr

  9. Phase-contrast x-ray computed tomography for biological imaging

    Science.gov (United States)

    Momose, Atsushi; Takeda, Tohoru; Itai, Yuji

    1997-10-01

    We have shown so far that 3D structures in biological sot tissues such as cancer can be revealed by phase-contrast x- ray computed tomography using an x-ray interferometer. As a next step, we aim at applications of this technique to in vivo observation, including radiographic applications. For this purpose, the size of view field is desired to be more than a few centimeters. Therefore, a larger x-ray interferometer should be used with x-rays of higher energy. We have evaluated the optimal x-ray energy from an aspect of does as a function of sample size. Moreover, desired spatial resolution to an image sensor is discussed as functions of x-ray energy and sample size, basing on a requirement in the analysis of interference fringes.

  10. 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.

  11. Exploratory survey of image quality on CR digital mammography imaging systems in Mexico

    International Nuclear Information System (INIS)

    Gaona, E.; Rivera, T.; Arreola, M.; Franco, J.; Molina, N.; Alvarez, B.; Azorín, C.G.; Casian, G.

    2014-01-01

    The purpose of this study was to assess the current status of image quality and dose in computed radiographic digital mammography (CRDM) systems. Studies included CRDM systems of various models and manufacturers which dose and image quality comparisons were performed. Due to the recent rise in the use of digital radiographic systems in Mexico, CRDM systems are rapidly replacing conventional film-screen systems without any regard to quality control or image quality standards. Study was conducted in 65 mammography facilities which use CRDM systems in the Mexico City and surrounding States. The systems were tested as used clinically. This means that the dose and beam qualities were selected using the automatic beam selection and photo-timed features. All systems surveyed generate laser film hardcopies for the radiologist to read on a scope or mammographic high luminance light box. It was found that 51 of CRDM systems presented a variety of image artefacts and non-uniformities arising from inadequate acquisition and processing, as well as from the laser printer itself. Undisciplined alteration of image processing settings by the technologist was found to be a serious prevalent problem in 42 facilities. Only four of them showed an image QC program which is periodically monitored by a medical physicist. The Average Glandular Dose (AGD) in the surveyed systems was estimated to have a mean value of 2.4 mGy. To improve image quality in mammography and make more efficient screening mammographic in early detection of breast cancer is required new legislation. - Highlights: • Radiation dose in CR digital mammography (CRDM) systems was determined. • Image quality related with dose in CR digital mammography (CRDM) systems was analysed. • Image processing artefacts were observed and correlated with dose. • Measured entrance dose by TL phosphors could be good parameter for radiation protection optimization in patient

  12. Developments of optical fast-gated imaging systems

    International Nuclear Information System (INIS)

    Koehler, H.A.; Kotecki, D.

    1984-08-01

    Several fast-gated imaging systems to measure ultra-fast single-transient data have been developed for time-resolved imaging of pulsed radiation sources. These systems were designed to achieve image recording times of 1 to 3 ms and dynamic ranges of >200:1 to produce large two-dimensional images (greater than or equal to 10 4 spatial points) of 1 to 2 ns exposure and small two-dimensional images (less than or equal to 200 spatial points) of less than or equal to 0.5 ns exposure. Both MCP intensified solid-state two-dimensional framing cameras and streak camera/solid-state camera systems were used; the framing camera system provides snap shots with high spatial resolution whereas the streak camera system provides for limited spatial points each with high temporal resolution. Applications of these systems include electron-beam, x-ray, gamma-ray, and neutron diagnostics. This report reviews the characteristics of the major components of fast-gated imaging systems developed at Lawrence Livermore National Laboratory. System performances are described in view of major experiments, and the diagnostic requirements of new experiments in atomic physics (x-ray lasers) and nuclear physics (fusion) are indicated

  13. Web tools for large-scale 3D biological images and atlases

    Directory of Open Access Journals (Sweden)

    Husz Zsolt L

    2012-06-01

    Full Text Available Abstract Background Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay. Results The standard Internet Imaging Protocol (IIP has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays. Conclusions Interactive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume.

  14. Function of dynamic models in systems biology: linking structure to behaviour.

    Science.gov (United States)

    Knüpfer, Christian; Beckstein, Clemens

    2013-10-08

    Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. In this paper we describe different functional aspects of dynamic models. This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets. Here we focus on how function links the structure and the behaviour of a model. Models play a specific role (teleological function) in the scientific process of finding explanations for dynamic phenomena. In order to fulfil this role a model has to be used in simulation experiments (pragmatical function). A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function). We claim that the function of dynamic models refers to both the simulation experiment executed by software (intrinsic function) and the biological experiment which produces the phenomena under investigation (extrinsic function). We use the presented conceptual framework for the function of dynamic models to review formal accounts for functional aspects of models in Systems Biology, such as checklists, ontologies, and formal languages. Furthermore, we identify missing formal accounts for some of the functional aspects. In order to fill one of these gaps we propose an ontology for the teleological function of models. We have thoroughly analysed the role and use of models in Systems Biology. The resulting conceptual framework for the function of models is an important first step towards a comprehensive formal representation of the functional knowledge involved in the modelling and simulation process

  15. Radiosynthesis and biological evaluation of 5-(3-[18F]Fluoropropyloxy)-L-tryptophan for tumor PET imaging

    International Nuclear Information System (INIS)

    He, Shanzhen; Tang, Ganghua; Hu, Kongzhen; Wang, Hongliang; Wang, Shuxia; Huang, Tingting; Liang, Xiang; Tang, Xiaolan

    2013-01-01

    Introduction: [ 18 F]FDG PET has difficulty distinguishing tumor from inflammation in the clinic because of the same high uptake in nonmalignant and inflammatory tissue. In contrast, amino acid tracers do not accumulate in inflamed tissues and thus provide an excellent opportunity for their use in clinical cancer imaging. In this study, we developed a new amino acid tracer 5-(3-[ 18 F]Fluoropropyloxy)-L-tryptophan ([ 18 F]-L-FPTP) by two-step reactions and performed its biologic evaluation. Methods: [ 18 F]-L-FPTP was prepared by [ 18 F]fluoropropylation of 5-hydroxy-L-tryptophan disodium salt and purification on C18 cartridges. The biodistribution of [ 18 F]-L-FPTP was determined in normal mice and the incorporation of [ 18 F]-L-FPTP into tissue proteins was investigated. In vitro competitive inhibition experiments were performed with Hepa1-6 hepatoma cell lines. [ 18 F]-L-FPTP PET imaging was performed on tumor-bearing and inflammation mice and compared with [ 18 F]-L-FEHTP PET. Results: The overall uncorrected radiochemical yield of [ 18 F]-L-FPTP was 21.1 ± 4.4% with a synthesis time of 60 min, the radiochemical purity was more than 99%. Biodistribution studies demonstrate high uptake of [ 18 F]-L-FPTP in liver, kidney, pancreas, and blood at the early phase, and fast clearance in most tissues over the whole observed time. The uptake studies in Hepa1-6 cells suggest that [ 18 F]-L-FPTP is transported by the amino acid transport system B 0,+ , LAT2 and ASC. [ 18 F]-L-FPTP displays good stability and is not incorporated into proteins in vitro. PET imaging shows that [ 18 F]-L-FPTP can be a better potential PET tracer for differentiating tumor from inflammation than [ 18 F]FDG and 5-(3-[ 18 F]fluoroethyloxy)-L-tryptophan ([ 18 F]-L-FEHTP), with high [ 18 F]-L-FPTP uptake ratio (2.53) of tumor to inflammation at 60 min postinjection. Conclusions: Using [ 18 F]fluoropropyl derivatives as intermediates, the new tracer [ 18 F]-L-FPTP was achieved with good yield and

  16. Biomedical Imaging Principles and Applications

    CERN Document Server

    Salzer, Reiner

    2012-01-01

    This book presents and describes imaging technologies that can be used to study chemical processes and structural interactions in dynamic systems, principally in biomedical systems. The imaging technologies, largely biomedical imaging technologies such as MRT, Fluorescence mapping, raman mapping, nanoESCA, and CARS microscopy, have been selected according to their application range and to the chemical information content of their data. These technologies allow for the analysis and evaluation of delicate biological samples, which must not be disturbed during the profess. Ultimately, this may me

  17. 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...

  18. Content Based Retrieval System for Magnetic Resonance Images

    International Nuclear Information System (INIS)

    Trojachanets, Katarina

    2010-01-01

    The amount of medical images is continuously increasing as a consequence of the constant growth and development of techniques for digital image acquisition. Manual annotation and description of each image is impractical, expensive and time consuming approach. Moreover, it is an imprecise and insufficient way for describing all information stored in medical images. This induces the necessity for developing efficient image storage, annotation and retrieval systems. Content based image retrieval (CBIR) emerges as an efficient approach for digital image retrieval from large databases. It includes two phases. In the first phase, the visual content of the image is analyzed and the feature extraction process is performed. An appropriate descriptor, namely, feature vector is then associated with each image. These descriptors are used in the second phase, i.e. the retrieval process. With the aim to improve the efficiency and precision of the content based image retrieval systems, feature extraction and automatic image annotation techniques are subject of continuous researches and development. Including the classification techniques in the retrieval process enables automatic image annotation in an existing CBIR system. It contributes to more efficient and easier image organization in the system.Applying content based retrieval in the field of magnetic resonance is a big challenge. Magnetic resonance imaging is an image based diagnostic technique which is widely used in medical environment. According to this, the number of magnetic resonance images is enormously growing. Magnetic resonance images provide plentiful medical information, high resolution and specific nature. Thus, the capability of CBIR systems for image retrieval from large database is of great importance for efficient analysis of this kind of images. The aim of this thesis is to propose content based retrieval system architecture for magnetic resonance images. To provide the system efficiency, feature

  19. Design of fluidized-bed, biological denitrification systems

    International Nuclear Information System (INIS)

    Patton, B.D.; Hancher, C.W.; Pitt, W.W.; Walker, J.F.

    1982-01-01

    Many commercial processes yield nitrate-containing wastewaters that are being discharged to the environment because traditional recovery or disposal methods are economically unacceptable. The anticipated discharge limits (i.e., 10 to 20 g (NO 3 - )/m 3 ) being considered by many states will not allow continued release of these wastewaters. The new discharge standards can be met economically by use of the fluidizied-bed, biological denitrification process. Research and development studies were conducted with 0.05-, 0.10-, 0.20-, and 0.50-m-diam fluidized-bed bioreactor systems. Feed nitrate concentrations were in the 0 to 10,000 g (NO 3 - )/m 3 range. Using the data from these studies, rate expressions were developed for the destruction of nitrate as a function of nitrate concentration. Methods were also developed for sizing bioreactors and biomass control systems. The sizing methods for fluidized-bed denitrification systems are described, and support systems such as sampling and analysis, instrumentation and controls, utilities, and bacteria storage are discussed. Operation of the process is also briefly discussed to aid the designer. Using the methods presented in this report, fluidized-bed, biological denitrification systems can be designed to treat nitrate wastewater streams

  20. 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)

  1. 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.

  2. Investigation of superharmonic sound propagation and imaging in biological tissues in vitro.

    Science.gov (United States)

    Ma, Qingyu; Zhang, Dong; Gong, Xiufen; Ma, Yong

    2006-04-01

    This article presents both theoretical and experimental studies on the superharmonic generation and its imaging in biological tissues. A superharmonic component is defined as a summation of the third-, fourth-, and fifth-order harmonics. A superharmonic signal is produced using an 8-mm-diam, 2.5-MHz planar piston source that is excited by eight-cycle, 2.5-MHz tone bursts. Axial and lateral field distributions of the superharmonic component and the second harmonic are first calculated based on the nonlinear KZK model and then compared with those experimentally determined at two different source pressures of 0.5 and 1 MPa. Results indicate that the amplitude of the superharmonic component can exceed that of the second harmonic, depending on the axial distance and the fundamental pressure amplitude. Also, the 3-dB beamwidth of the superharmonic component is about 23% narrower than that of the second harmonic. Additional experiments are performed in vitro using liver and fatty tissues in transmission mode and produced two-dimensional images using the fundamental, the second harmonic, and the superharmonic signals. Although the clinical applicability of this work still needs to be assessed, these results indicate that the superharmonic image quality is better than that of the other two images.

  3. 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.

  4. Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems

    Science.gov (United States)

    Cerbino, Roberto; Cicuta, Pietro

    2017-09-01

    Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.

  5. Design and simulation of a totally digital image system for medical image applications

    International Nuclear Information System (INIS)

    Archwamety, C.

    1987-01-01

    The Totally Digital Imaging System (TDIS) is based on system requirements information from the Radiology Department, University of Arizona Health Science Center. This dissertation presents the design of this complex system, the TDIS specification, the system performance requirements, and the evaluation of the system using the computer-simulation programs. Discrete-event simulation models were developed for the TDIS subsystems, including an image network, imaging equipment, storage migration algorithm, data base archive system, and a control and management network. The simulation system uses empirical data generation and retrieval rates measured at the University Medical Center hospital. The entire TDIS system was simulated in Simscript II.5 using a VAX 8600 computer system. Simulation results show the fiber-optical-image network to be suitable; however, the optical-disk-storage system represents a performance bottleneck

  6. 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.

  7. 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.

  8. Mathematical computer simulation of the process of ultrasound interaction with biological medium

    International Nuclear Information System (INIS)

    Yakovleva, T.; Nassiri, D.; Ciantar, D.

    1996-01-01

    The aim of the paper is to study theoretically the interaction of ultrasound irradiation with biological medium and the peculiarities of ultrasound scattering by inhomogeneities of biological tissue, which can be represented by fractal structures. This investigation has been used for the construction of the computer model of three-dimensional ultrasonic imaging system what gives the possibility to define more accurately the pathological changes in such a tissue by means of its image analysis. Poster 180. (author)

  9. Simultaneous biological nutrient removal: evaluation of autotrophic denitrification, heterotrophic nitrification, and biological phosphorus removal in full-scale systems.

    Science.gov (United States)

    Littleton, Helen X; Daigger, Glen T; Strom, Peter F; Cowan, Robert A

    2003-01-01

    Simultaneous biological nutrient removal (SBNR) is the biological removal of nitrogen and phosphorus in excess of that required for biomass synthesis in a biological wastewater treatment system without defined anaerobic or anoxic zones. Evidence is growing that significant SBNR can occur in many systems, including the aerobic zone of systems already configured for biological nutrient removal. Although SBNR systems offer several potential advantages, they cannot be fully realized until the mechanisms responsible for SBNR are better understood. Consequently, a research program was initiated with the basic hypothesis that three mechanisms might be responsible for SBNR: the reactor macroenvironment, the floc microenvironment, and novel microorganisms. Previously, the nutrient removal capabilities of seven full-scale, staged, closed-loop bioreactors known as Orbal oxidation ditches were evaluated. Chemical analysis and microbiological observations suggested that SBNR occurred in these systems. Three of these plants were further examined in this research to evaluate the importance of novel microorganisms, especially for nitrogen removal. A screening tool was developed to determine the relative significance of the activities of microorganisms capable of autotrophic denitrification and heterotrophic nitrification-aerobic denitrification in biological nutrient removal systems. The results indicated that novel microorganisms were not substantial contributors to SBNR in the plants studied. Phosphorus metabolism (anaerobic release, aerobic uptake) was also tested in one of the plants. Activity within the mixed liquor that was consistent with current theories for phosphorus-accumulating organisms (PAOs) was observed. Along with other observations, this suggests the presence of PAOs in the facilities studied.

  10. 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.

  11. Mathematical models in biology bringing mathematics to life

    CERN Document Server

    Ferraro, Maria; Guarracino, Mario

    2015-01-01

    This book presents an exciting collection of contributions based on the workshop “Bringing Maths to Life” held October 27-29, 2014 in Naples, Italy.  The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content...

  12. Two faces of entropy and information in biological systems.

    Science.gov (United States)

    Mitrokhin, Yuriy

    2014-10-21

    The article attempts to overcome the well-known paradox of contradictions between the emerging biological organization and entropy production in biological systems. It is assumed that quality, speculative correlation between entropy and antientropy processes taking place both in the past and today in the metabolic and genetic cellular systems may be perfectly authorized for adequate description of the evolution of biological organization. So far as thermodynamic entropy itself cannot compensate for the high degree of organization which exists in the cell, we discuss the mode of conjunction of positive entropy events (mutations) in the genetic systems of the past generations and the formation of organized structures of current cells. We argue that only the information which is generated in the conditions of the information entropy production (mutations and other genome reorganization) in genetic systems of the past generations provides the physical conjunction of entropy and antientropy processes separated from each other in time generations. It is readily apparent from the requirements of the Second law of thermodynamics. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. 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.

  14. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

    Science.gov (United States)

    Moodie, Stuart; Le Novère, Nicolas; Demir, Emek; Mi, Huaiyu; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  15. 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.

  16. 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...

  17. Imaging of pharmacokinetic rates of indocyanine green in mouse liver with a hybrid fluorescence molecular tomography/x-ray computed tomography system.

    Science.gov (United States)

    Zhang, Guanglei; Liu, Fei; Zhang, Bin; He, Yun; Luo, Jianwen; Bai, Jing

    2013-04-01

    Pharmacokinetic rates have the potential to provide quantitative physiological and pathological information for biological studies and drug development. Fluorescence molecular tomography (FMT) is an attractive imaging tool for three-dimensionally resolving fluorophore distribution in small animals. In this letter, pharmacokinetic rates of indocyanine green (ICG) in mouse liver are imaged with a hybrid FMT and x-ray computed tomography (XCT) system. A recently developed FMT method using structural priors from an XCT system is adopted to improve the quality of FMT reconstruction. In the in vivo experiments, images of uptake and excretion rates of ICG in mouse liver are obtained, which can be used to quantitatively evaluate liver function. The accuracy of the results is validated by a fiber-based fluorescence measurement system.

  18. 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.

  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. An image analysis system for near-infrared (NIR) fluorescence lymph imaging

    Science.gov (United States)

    Zhang, Jingdan; Zhou, Shaohua Kevin; Xiang, Xiaoyan; Rasmussen, John C.; Sevick-Muraca, Eva M.

    2011-03-01

    Quantitative analysis of lymphatic function is crucial for understanding the lymphatic system and diagnosing the associated diseases. Recently, a near-infrared (NIR) fluorescence imaging system is developed for real-time imaging lymphatic propulsion by intradermal injection of microdose of a NIR fluorophore distal to the lymphatics of interest. However, the previous analysis software3, 4 is underdeveloped, requiring extensive time and effort to analyze a NIR image sequence. In this paper, we develop a number of image processing techniques to automate the data analysis workflow, including an object tracking algorithm to stabilize the subject and remove the motion artifacts, an image representation named flow map to characterize lymphatic flow more reliably, and an automatic algorithm to compute lymph velocity and frequency of propulsion. By integrating all these techniques to a system, the analysis workflow significantly reduces the amount of required user interaction and improves the reliability of the measurement.

  1. 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…

  2. Tissue Equivalent Phantom Design for Characterization of a Coherent Scatter X-ray Imaging System

    Science.gov (United States)

    Albanese, Kathryn Elizabeth

    Scatter in medical imaging is typically cast off as image-related noise that detracts from meaningful diagnosis. It is therefore typically rejected or removed from medical images. However, it has been found that every material, including cancerous tissue, has a unique X-ray coherent scatter signature that can be used to identify the material or tissue. Such scatter-based tissue-identification provides the advantage of locating and identifying particular materials over conventional anatomical imaging through X-ray radiography. A coded aperture X-ray coherent scatter spectral imaging system has been developed in our group to classify different tissue types based on their unique scatter signatures. Previous experiments using our prototype have demonstrated that the depth-resolved coherent scatter spectral imaging system (CACSSI) can discriminate healthy and cancerous tissue present in the path of a non-destructive x-ray beam. A key to the successful optimization of CACSSI as a clinical imaging method is to obtain anatomically accurate phantoms of the human body. This thesis describes the development and fabrication of 3D printed anatomical scatter phantoms of the breast and lung. The purpose of this work is to accurately model different breast geometries using a tissue equivalent phantom, and to classify these tissues in a coherent x-ray scatter imaging system. Tissue-equivalent anatomical phantoms were designed to assess the capability of the CACSSI system to classify different types of breast tissue (adipose, fibroglandular, malignant). These phantoms were 3D printed based on DICOM data obtained from CT scans of prone breasts. The phantoms were tested through comparison of measured scatter signatures with those of adipose and fibroglandular tissue from literature. Tumors in the phantom were modeled using a variety of biological tissue including actual surgically excised benign and malignant tissue specimens. Lung based phantoms have also been printed for future

  3. Systems Biology of Immune Response to Live and Inactivated Dengue Virus Vaccines

    Science.gov (United States)

    2017-09-01

    AWARD NUMBER: W81XWH-16-2-0032 TITLE: Systems Biology of Immune Response to Live and Inactivated Dengue Virus Vaccines PRINCIPAL INVESTIGATOR...CONTRACT NUMBER Systems Biology of Immune Response to Live and Inactivated Dengue Virus Vaccines 5b. GRANT NUMBER W81XWH-16-2-0032 5c. PROGRAM ELEMENT...cell) responses will be measured using molecular and cellular approaches and the data analyzed using a systems biology approach. During the first

  4. 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

  5. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

    Science.gov (United States)

    Hucka, M; Finney, A; Bornstein, B J; Keating, S M; Shapiro, B E; Matthews, J; Kovitz, B L; Schilstra, M J; Funahashi, A; Doyle, J C; Kitano, H

    2004-06-01

    Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

  6. What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform

    NARCIS (Netherlands)

    Swat, Maciej; Kiełbasa, Szymon M.; Polak, Sebastian; Olivier, Brett; Bruggeman, Frank J.; Tulloch, Mark Quinton; Snoep, Jacky L.; Verhoeven, Arthur J.; Westerhoff, Hans V.

    2011-01-01

    The utility of model repositories is discussed in the context of systems biology (SB). It is shown how such repositories, and in particular their live versions, can be used for computational SB: we calculate the robustness of the yeast glycolytic network with respect to perturbations of one of its

  7. 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...

  8. Integrative systems and synthetic biology of cell-matrix adhesion sites.

    Science.gov (United States)

    Zamir, Eli

    2016-09-02

    The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.

  9. Recent technologic developments on high-resolution beta imaging systems for quantitative autoradiography and double labeling applications

    CERN Document Server

    Barthe, N; Chatti, K; Coulon, P; Maitrejean, S; 10.1016/j.nima.2004.03.014

    2004-01-01

    Two novel beta imaging systems, particularly interesting in the field of radiopharmacology and molecular biology research, were developed these last years. (1) a beta imager was derived from research conducted by Pr Charpak at CERN. This parallel plate avalanche chamber is a direct detection system of beta radioactivity, which is particularly adapted for qualitative and quantitative autoradiography. With this detector, autoradiographic techniques can be performed with emitters such as /sup 99m/Tc because this radionuclide emits many low-energy electrons and the detector has a very low sensitivity to low-range gamma -rays. Its sensitivity (smallest activity detected: 0.007 cpm/mm/sup 2/ for /sup 3/H and 0.01 for /sup 14/C), linearity (over a dynamic range of 10/sup 4/) and spatial resolution (50 mu m for /sup 3/H or /sup 99m/Tc to 150 mu m for /sup 32/P or /sup 18/F ( beta /sup +/)) gives a real interest to this system as a new imaging device. Its principle of detection is based on the analysis of light emitte...

  10. Consultation system for image diagnosis: Report formation support system

    International Nuclear Information System (INIS)

    Ikeda, M.; Sakuma, S.; Ishigaki, T.; Suzuki, K.; Oikawa, K.

    1987-01-01

    The authors developed a consultation system for image diagnosis, involving artificial intelligence ideas. In this system, the authors proposed a new report formation support system and implemented it in lymphangiography. This support system starts with the input of image interpretation. The input process is made mainly by selecting items. This system encodes the input findings into the semantic network, which is represented as a directed graph, and it reserves them into the knowledge database in the above structure. Finally, the output (report) is made in the near natural language, which corresponds to the input findings

  11. Digital radiology and digitally formatted image management systems

    International Nuclear Information System (INIS)

    Cox, G.G.; Dwyer, S.J. III; Templeton, A.W.

    1987-01-01

    The number of diagnostic examinations performed with digitally formatted imaging equipment is increasing. Digital general-purpose and fluoroscopic radiology systems are being clinically evaluated. Digitizing conventional x-ray films, such as mammograms, frequently improves the diagnostic quality of the images. The digitizing process with laser has also afforded the opportunity to document required spatial resolution for digital imaging and network systems. The use of digitally formatted image instrumentation imposes new requirements on the acquisition, display and manipulation, transmission, hard copy image recording, and archiving of diagnostic data. Networking of digitally formatted image data offers many advantages for managing digital information. This paper identifies and describes digital radiographic systems. Parameters required for designing and implementing a digital image management system are outlined. Spatial and contrast resolution requirements are identified. The key parameters include the amount of image data generated each working day, the retrieval rate of the generated data, the display hardware and software needed for interactive diagnosis display stations, the requirements for analog hard copy generation, and on-line and long-term archiving requirements. These image management systems are often called PACS (Picture Archiving and Communication Systems)

  12. The correlation between biological activity and diffusion-weighted MR imaging and ADC value in cases with prostate cancer.

    Science.gov (United States)

    Sokmen, Bedriye Koyuncu; Sokmen, Dogukan; Ucar, Nese; Ozkurt, Huseyin; Simsek, Abdulmuttalip

    2017-12-31

    Firstly, we aimed to investigate the correlation among dynamic contrasted magnetic resonance (MR) images, diffusion-weighted MR images, and apparent diffusion coefficent (ADC) values in patients with prostate cancer. Secondly, we aimed to investigate the roles of these variables on clinical risk classification and the biological behavior of the prostate cancer. A total of sixty with prostatic adenocarcinoma patients diagnosed between January 2011 and May 2013 were retrospectively included in the study. Risk classification of patients were evaluated as low-risk (Group 1) (n = 20) (Stage T1c-T2a, PSA T3a, PSA > 20 ng/ml, Gleason Score > 7). Diffusion-weighted MR images, dynamic contrasted MR images, and ADC values of the prostates were correlated. ADC values of the cases in Group 3 were lower than those of the other groups (p values of the areas without malignancy did not differ significantly between groups (p > 0.05). Biological activity of the tumor tissue was determined by GS, while a negative correlation was observed between GSs and ADC values of the patients, (p values were obtained. These measured values can play a role in the noninvasive determination of the cellularity of the tumoral mass.

  13. Real-Time Tracking the Synthesis and Degradation of Albumin in Complex Biological Systems with a near-Infrared Fluorescent Probe.

    Science.gov (United States)

    Jin, Qiang; Feng, Lei; Zhang, Shui-Jun; Wang, Dan-Dan; Wang, Fang-Jun; Zhang, Yi; Cui, Jing-Nan; Guo, Wen-Zhi; Ge, Guang-Bo; Yang, Ling

    2017-09-19

    In this study, a novel fluorescent detection system for biological sensing of human albumin (HA) was developed on the basis of the pseudoesterase activity and substrate preference of HA. The designed near-infrared (NIR) fluorescent probe (DDAP) could be effectively hydrolyzed by HA, accompanied by significant changes in both color and fluorescence spectrum. The sensing mechanism was fully investigated by fluorescence spectroscopy, NMR, and mass spectra. DDAP exhibited excellent selectivity and sensitivity toward HA over a variety of human plasma proteins, hydrolases, and abundant biomolecules found in human body. The probe has been successfully applied to measure native HA in diluted plasma samples and the secreted HA in the hepatocyte culture supernatant. DDAP has also been used for fluorescence imaging of HA reabsorption in living renal cells, and the results show that the probe exhibits good cell permeability, low cytotoxicity and high imaging resolution. Furthermore, DDAP has been successfully used for real-time tracking the uptaking and degradation of albumin in ex vivo mouse kidney models for the first time. All these results clearly demonstrated that DDAP-based assay held great promise for real-time sensing and tracking HA in complex biological systems, which would be very useful for basic researches and clinical diagnosis of HA-associated diseases.

  14. Boolean modeling in systems biology: an overview of methodology and applications

    International Nuclear Information System (INIS)

    Wang, Rui-Sheng; Albert, Réka; Saadatpour, Assieh

    2012-01-01

    Mathematical modeling of biological processes provides deep insights into complex cellular systems. While quantitative and continuous models such as differential equations have been widely used, their use is obstructed in systems wherein the knowledge of mechanistic details and kinetic parameters is scarce. On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the experimental literature and high-throughput technologies, making qualitative approaches such as Boolean network modeling extremely useful. In this paper, we build on our research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models. We finally demonstrate how Boolean models can be applied to perform the structural analysis of cellular networks. This overview aims to acquaint life science researchers with the basic steps of Boolean modeling and its applications in several areas of systems biology. (paper)

  15. Converting differential-equation models of biological systems to membrane computing.

    Science.gov (United States)

    Muniyandi, Ravie Chandren; Zin, Abdullah Mohd; Sanders, J W

    2013-12-01

    This paper presents a method to convert the deterministic, continuous representation of a biological system by ordinary differential equations into a non-deterministic, discrete membrane computation. The dynamics of the membrane computation is governed by rewrite rules operating at certain rates. That has the advantage of applying accurately to small systems, and to expressing rates of change that are determined locally, by region, but not necessary globally. Such spatial information augments the standard differentiable approach to provide a more realistic model. A biological case study of the ligand-receptor network of protein TGF-β is used to validate the effectiveness of the conversion method. It demonstrates the sense in which the behaviours and properties of the system are better preserved in the membrane computing model, suggesting that the proposed conversion method may prove useful for biological systems in particular. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  16. 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.

  17. 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

  18. Quantum mechanical simulation methods for studying biological systems

    International Nuclear Information System (INIS)

    Bicout, D.; Field, M.

    1996-01-01

    Most known biological mechanisms can be explained using fundamental laws of physics and chemistry and a full understanding of biological processes requires a multidisciplinary approach in which all the tools of biology, chemistry and physics are employed. An area of research becoming increasingly important is the theoretical study of biological macromolecules where numerical experimentation plays a double role of establishing a link between theoretical models and predictions and allowing a quantitative comparison between experiments and models. This workshop brought researchers working on different aspects of the development and application of quantum mechanical simulation together, assessed the state-of-the-art in the field and highlighted directions for future research. Fourteen lectures (theoretical courses and specialized seminars) deal with following themes: 1) quantum mechanical calculations of large systems, 2) ab initio molecular dynamics where the calculation of the wavefunction and hence the energy and forces on the atoms for a system at a single nuclear configuration are combined with classical molecular dynamics algorithms in order to perform simulations which use a quantum mechanical potential energy surface, 3) quantum dynamical simulations, electron and proton transfer processes in proteins and in solutions and finally, 4) free seminars that helped to enlarge the scope of the workshop. (N.T.)

  19. [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.

  20. Hybrid imaging: Instrumentation and Data Processing

    Science.gov (United States)

    Cal-Gonzalez, Jacobo; Rausch, Ivo; Shiyam Sundar, Lalith K.; Lassen, Martin L.; Muzik, Otto; Moser, Ewald; Papp, Laszlo; Beyer, Thomas

    2018-05-01

    State-of-the-art patient management frequently requires the use of non-invasive imaging methods to assess the anatomy, function or molecular-biological conditions of patients or study subjects. Such imaging methods can be singular, providing either anatomical or molecular information, or they can be combined, thus, providing "anato-metabolic" information. Hybrid imaging denotes image acquisitions on systems that physically combine complementary imaging modalities for an improved diagnostic accuracy and confidence as well as for increased patient comfort. The physical combination of formerly independent imaging modalities was driven by leading innovators in the field of clinical research and benefited from technological advances that permitted the operation of PET and MR in close physical proximity, for example. This review covers milestones of the development of various hybrid imaging systems for use in clinical practice and small-animal research. Special attention is given to technological advances that helped the adoption of hybrid imaging, as well as to introducing methodological concepts that benefit from the availability of complementary anatomical and biological information, such as new types of image reconstruction and data correction schemes. The ultimate goal of hybrid imaging is to provide useful, complementary and quantitative information during patient work-up. Hybrid imaging also opens the door to multi-parametric assessment of diseases, which will help us better understand the causes of various diseases that currently contribute to a large fraction of healthcare costs.