WorldWideScience

Sample records for biological dosimetry network

  1. The Latin American Biological Dosimetry Network (LBDNet)

    International Nuclear Information System (INIS)

    Garcia, O.; Lamadrid, A.I.; Gonzalez, J.E.; Romero, I.; Mandina, T.; Di Giorgio, M.; Radl, A.; Taja, M.R.; Sapienza, C.E.; Deminge, M.M.; Fernandez Rearte, J.; Stuck Oliveira, M.; Valdivia, P.; Guerrero-Carbajal, C.; Arceo Maldonado, C.; Cortina Ramirez, G.E.; Espinoza, M.; Martinez-Lopez, W.; Di Tomasso, M.

    2016-01-01

    Biological Dosimetry is a necessary support for national radiation protection programmes and emergency response schemes. The Latin American Biological Dosimetry Network (LBDNet) was formally founded in 2007 to provide early biological dosimetry assistance in case of radiation emergencies in the Latin American Region. Here are presented the main topics considered in the foundational document of the network, which comprise: mission, partners, concept of operation, including the mechanism to request support for biological dosimetry assistance in the region, and the network capabilities. The process for network activation and the role of the coordinating laboratory during biological dosimetry emergency response is also presented. This information is preceded by historical remarks on biological dosimetry cooperation in Latin America. A summary of the main experimental and practical results already obtained by the LBDNet is also included. (authors)

  2. The Latin American Biological Dosimetry Network (LBDNet).

    Science.gov (United States)

    García, O; Di Giorgio, M; Radl, A; Taja, M R; Sapienza, C E; Deminge, M M; Fernández Rearte, J; Stuck Oliveira, M; Valdivia, P; Lamadrid, A I; González, J E; Romero, I; Mandina, T; Guerrero-Carbajal, C; ArceoMaldonado, C; Cortina Ramírez, G E; Espinoza, M; Martínez-López, W; Di Tomasso, M

    2016-09-01

    Biological Dosimetry is a necessary support for national radiation protection programmes and emergency response schemes. The Latin American Biological Dosimetry Network (LBDNet) was formally founded in 2007 to provide early biological dosimetry assistance in case of radiation emergencies in the Latin American Region. Here are presented the main topics considered in the foundational document of the network, which comprise: mission, partners, concept of operation, including the mechanism to request support for biological dosimetry assistance in the region, and the network capabilities. The process for network activation and the role of the coordinating laboratory during biological dosimetry emergency response is also presented. This information is preceded by historical remarks on biological dosimetry cooperation in Latin America. A summary of the main experimental and practical results already obtained by the LBDNet is also included. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. RENEB - Running the European Network of biological dosimetry and physical retrospective dosimetry.

    Science.gov (United States)

    Kulka, Ulrike; Abend, Michael; Ainsbury, Elizabeth; Badie, Christophe; Barquinero, Joan Francesc; Barrios, Lleonard; Beinke, Christina; Bortolin, Emanuela; Cucu, Alexandra; De Amicis, Andrea; Domínguez, Inmaculada; Fattibene, Paola; Frøvig, Anne Marie; Gregoire, Eric; Guogyte, Kamile; Hadjidekova, Valeria; Jaworska, Alicja; Kriehuber, Ralf; Lindholm, Carita; Lloyd, David; Lumniczky, Katalin; Lyng, Fiona; Meschini, Roberta; Mörtl, Simone; Della Monaca, Sara; Monteiro Gil, Octávia; Montoro, Alegria; Moquet, Jayne; Moreno, Mercedes; Oestreicher, Ursula; Palitti, Fabrizio; Pantelias, Gabriel; Patrono, Clarice; Piqueret-Stephan, Laure; Port, Matthias; Prieto, María Jesus; Quintens, Roel; Ricoul, Michelle; Romm, Horst; Roy, Laurence; Sáfrány, Géza; Sabatier, Laure; Sebastià, Natividad; Sommer, Sylwester; Terzoudi, Georgia; Testa, Antonella; Thierens, Hubert; Turai, Istvan; Trompier, François; Valente, Marco; Vaz, Pedro; Voisin, Philippe; Vral, Anne; Woda, Clemens; Zafiropoulos, Demetre; Wojcik, Andrzej

    2017-01-01

    A European network was initiated in 2012 by 23 partners from 16 European countries with the aim to significantly increase individualized dose reconstruction in case of large-scale radiological emergency scenarios. The network was built on three complementary pillars: (1) an operational basis with seven biological and physical dosimetric assays in ready-to-use mode, (2) a basis for education, training and quality assurance, and (3) a basis for further network development regarding new techniques and members. Techniques for individual dose estimation based on biological samples and/or inert personalized devices as mobile phones or smart phones were optimized to support rapid categorization of many potential victims according to the received dose to the blood or personal devices. Communication and cross-border collaboration were also standardized. To assure long-term sustainability of the network, cooperation with national and international emergency preparedness organizations was initiated and links to radiation protection and research platforms have been developed. A legal framework, based on a Memorandum of Understanding, was established and signed by 27 organizations by the end of 2015. RENEB is a European Network of biological and physical-retrospective dosimetry, with the capacity and capability to perform large-scale rapid individualized dose estimation. Specialized to handle large numbers of samples, RENEB is able to contribute to radiological emergency preparedness and wider large-scale research projects.

  4. Latinamerican Biological Dosimetry Network (LBDNET). International Biological Dosimetry intercomparison Program (exercise 2007-2008)

    International Nuclear Information System (INIS)

    Di Giorgio, Marina; Vallerga, Maria B.; Radl, A.; Taja, Maria R.

    2009-01-01

    This paper describes the International Biological Dosimetry Intercomparison Program (exercise 2007-2008) - developed within the framework of the IAEA regional project - RLA/9/054 (Establishment of national capabilities for response to radiological and nuclear emergency) whose general objectives are: assess reproducibility inter-laboratory; identify problems and provide the necessary modifications for collaborative work in accidental situations requiring activation of mutual assistance mechanisms which will form the basis of the Organization of LBDNET. This exercise involves the laboratories of the region: Argentina (laboratory support), Brazil, Chile, Cuba, Mexico, Peru and Uruguay and the laboratory of the Autonomous University of Barcelona-Espana (Joan Francesc Barquinero and staff). Finally, these countries will meet the next time for the drafting of a final report and later publication. (author)

  5. Canadian Cytogenetic Emergency network (CEN) for biological dosimetry following radiological/nuclear accidents.

    Science.gov (United States)

    Miller, Susan M; Ferrarotto, Catherine L; Vlahovich, Slavica; Wilkins, Ruth C; Boreham, Douglas R; Dolling, Jo-Anna

    2007-07-01

    To test the ability of the cytogenetic emergency network (CEN) of laboratories, currently under development across Canada, to provide rapid biological dosimetry using the dicentric assay for triage assessment, that could be implemented in the event of a large-scale radiation/nuclear emergency. A workshop was held in May 2004 in Toronto, Canada, to introduce the concept of CEN and recruit clinical cytogenetic laboratories at hospitals across the country. Slides were prepared for dicentric assay analysis following in vitro irradiation of blood to a range of gamma-ray doses. A minimum of 50 metaphases per slide were analyzed by 41 people at 22 different laboratories to estimate the exposure level. Dose estimates were calculated based on a dose response curve generated at Health Canada. There were a total of 104 dose estimates and 96 (92.3%) of them fell within the expected range using triage scoring criteria. Half of the laboratories analyzed 50 metaphases in network were acceptable for emergency biological dosimetry. When this network is fully operational, it will be the first of its kind in Canada able to respond to radiological/nuclear emergencies by providing triage quality biological dosimetry for a large number of samples. This network represents an alternate expansion of existing international emergency biological dosimetry cytogenetic networks.

  6. Main activities of the Latin American Network of Biological Dosimetry (LBDNet)

    International Nuclear Information System (INIS)

    Di Giorgio, M.; Vallerga, M.B.; Radl, A.; Taja, M.R.; Stuck Oliveira, M.; Valdivia, P.; Garcia Lima, O.; Lamadrid, A.; Gonzalez Mesa, J.E.; Romero Aguilera, I.; Mandina Cardoso, T.; Guerrero Carbajal, C.; Arceo Maldonado, C.; Espinoza, M.; Martinez Lopez, W.; Di Tomasso, M.; Barquinero, F.; Roy, L.

    2010-01-01

    The Latin American Biological Dosimetry Network (LBDNET) was constituted in 2007 for mutual assistance in case of a radiation emergency in the region supported by IAEA Technical Cooperation Projects RLA/9/054 and RLA/9/061. The main objectives are: a) to strengthen the technical capacities of Biological Dosimetry Services belonging to laboratories existing in the region (Argentine, Brazil, Chile, Cuba, Mexico, Peru and Uruguay) integrated in National Radiological Emergency Plans to provide a rapid biodosimetric response in a coordinated manner between countries and with RANET-IAEA/BioDoseNet-WHO, b) to provide support to other countries in the region lacking Biological Dosimetry laboratories, c) to consolidate the organization of the Latin American Biological Dosimetry Network for mutual assistance. The activities developed include technical meetings for protocols and chromosomal aberration scoring criteria unification, blood samples cultures exercises, chromosomal aberrations analysis at microscope, discussion of statistical methods and specialized software for dose calculation, the intercomparison between laboratory data after the analysis of slides with irradiated material and the intercomparison of the analysis of captured images distributed electronically in the WEB. The last exercise was the transportation of an irradiated human blood sample to countries inside and outside of the region. At the moment the exercises are concluded and they are pending to be published in reference journals. Results obtained show the capacity in the region for a biodosimetric response to a radiological accident. In the future the network will integrate techniques for high dose exposure evaluation and will enhance the interaction with other emergency systems in the region. (authors) [es

  7. The Latin American Biological Dosimetry Network (LBDNet): Argentina, Brazil, Chile, Cuba, Mexico, Peru, Uruguay

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero C, C.; Arceo M, C. [ININ, Carretera Mexico-Toluca s/n, Ocoyoacac 52750, Estado de Mexico (Mexico); Di Giorgio, M.; Vallerga, M.; Radl, A. [Autoridad Regulatoria Nuclear, Av. del Libertador 8250, C1429 BNP CABA (Argentina); Taja, M.; Seoane, A.; De Luca, J. [Universidad Nacionald de La Plata, Av. 7 No. 1776, La Plata 1900, Buenos Aires (Argentina); Stuck O, M. [Instituto de Radioproteccion y Dosimetria, Av. Salvador Allende s/n, Recreio dos Bandeirantes, Rio de Janeiro (Brazil); Valdivia, P., E-mail: lbdnet@googlegroups.co [Comision Chilena de Energia, Amutanegui 95, Santiago Centro, Santiago (Chile)

    2010-10-15

    Biological dosimetry is a necessary support for national radiation protection programs and emergency response schemes. The Latin American Biological Dosimetry Network (LBDNet) was formally founded in 2007 for mutual assistance in case of radiation emergencies and for providing support to other Latin American countries that do not have bio dosimetry laboratories. In the frame of the IAEA Technical Cooperation Projects RLA/9/54 and RLA/9/61 the following activities have been performed: a) An international intercomparison exercise organized during 2007-2008 included six European countries and LBDNet laboratories. Relevant parameters related with dose assessment were evaluated through triage and conventional scoring criteria. A new approach for statistical data analysis was developed including assessment of inter-laboratory reproducibility and intra-laboratory repeatability. Overall, the laboratory performance was satisfactory for mutual cooperation purposes. b) In 2009, LBDNet and two European countries carried out a digital image intercomparison exercise involving dose assessment from metaphase images distributed electronically through internet. The main objectives were to evaluate scoring feasibility on metaphase images and time response. In addition a re-examination phase was considered in which the most controversial images were discussed jointly, this allowed for the development of a homogeneous scoring criteria within the network. c) A further exercise was performed during 2009 involving the shipment of biological samples for biological dosimetry assessment. The aim of this exercise was to test the timely and properly sending and receiving blood samples under national and international regulations. A total of 14 laboratories participated in this joint IAEA, PAHO and WHO. (Author)

  8. The Latin American Biological Dosimetry Network (LBDNet): Argentina, Brazil, Chile, Cuba, Mexico, Peru, Uruguay

    International Nuclear Information System (INIS)

    Guerrero C, C.; Arceo M, C.; Di Giorgio, M.; Vallerga, M.; Radl, A.; Taja, M.; Seoane, A.; De Luca, J.; Stuck O, M.; Valdivia, P.

    2010-10-01

    Biological dosimetry is a necessary support for national radiation protection programs and emergency response schemes. The Latin American Biological Dosimetry Network (LBDNet) was formally founded in 2007 for mutual assistance in case of radiation emergencies and for providing support to other Latin American countries that do not have bio dosimetry laboratories. In the frame of the IAEA Technical Cooperation Projects RLA/9/54 and RLA/9/61 the following activities have been performed: a) An international intercomparison exercise organized during 2007-2008 included six European countries and LBDNet laboratories. Relevant parameters related with dose assessment were evaluated through triage and conventional scoring criteria. A new approach for statistical data analysis was developed including assessment of inter-laboratory reproducibility and intra-laboratory repeatability. Overall, the laboratory performance was satisfactory for mutual cooperation purposes. b) In 2009, LBDNet and two European countries carried out a digital image intercomparison exercise involving dose assessment from metaphase images distributed electronically through internet. The main objectives were to evaluate scoring feasibility on metaphase images and time response. In addition a re-examination phase was considered in which the most controversial images were discussed jointly, this allowed for the development of a homogeneous scoring criteria within the network. c) A further exercise was performed during 2009 involving the shipment of biological samples for biological dosimetry assessment. The aim of this exercise was to test the timely and properly sending and receiving blood samples under national and international regulations. A total of 14 laboratories participated in this joint IAEA, PAHO and WHO. (Author)

  9. Latin-American Biological Dosimetry Network (LBDNET) Intercomparison Exercise. Evaluation through triage and conventional scoring criteria. Development of a new approach for statistical data analysis

    International Nuclear Information System (INIS)

    Di Giorgio, M.; Vallerga, M.B.; Radl, A.

    2011-01-01

    Biological Dosimetry is a necessary support for National Radiation Protection Programs and Emergency Response Schemes. A Latin-American Biological Dosimetry Network (LBDNET) has been constituted by the biological dosimetry laboratories from: Argentina, Brazil, Chile, Cuba, Mexico, Peru, and Uruguay (IAEA Regional Project RLA9/054, 2007). The biological dosimetry laboratory of Argentina organized an international biological dosimetry intercomparison for the analysis of some relevant parameters involved in dose assessment, to reinforce the response capability in accidental situations requiring the activation of mutual assistance mechanisms and thus, constituting the bases of the LBDNET organization. (authors)

  10. Neutron dosimetry in biology

    International Nuclear Information System (INIS)

    Sigurbjoernsson, B.; Smith, H.H.; Gustafsson, A.

    1965-01-01

    To study adequately the biological effects of different energy neutrons it is necessary to have high-intensity sources which are not contaminated by other radiations, the most serious of which are gamma rays. An effective dosimetry must provide an accurate measure of the absorbed dose, in biological materials, of each type of radiation at any reactor facility involved in radiobiological research. A standardized biological dosimetry, in addition to physical and chemical methods, may be desirable. The ideal data needed to achieve a fully documented dosimetry has been compiled by H. Glubrecht: (1) Energy spectrum and intensity of neutrons; (2) Angular distribution of neutrons on the whole surface of the irradiated object; (3) Additional undesired radiation accompanying the neutrons; (4) Physical state and chemical composition of the irradiated object. It is not sufficient to note only an integral dose value (e.g. in 'rad') as the biological effect depends on the above data

  11. Biological dosimetry by the triage dicentric chromosome assay - Further validation of international networking

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Ruth C., E-mail: Ruth.Wilkins@hc-sc.gc.ca [Health Canada, Ottawa, ON K1A 0K9 (Canada); Romm, Horst; Oestreicher, Ursula [Bundesamt fur Strahlenschutz, 38226 Salzgitter (Germany); Marro, Leonora [Health Canada, Ottawa, ON K1A 0K9 (Canada); Yoshida, Mitsuaki A. [Biological Dosimetry Section, Dept. of Dose Assessment, Research Center for Radiation Emergency Medicine, NIRS, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Department Radiation Biology, Institute of Radiation Emergency Medicine, Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki, Aomori 036-8564 (Japan); Suto, Y. [Biological Dosimetry Section, Dept. of Dose Assessment, Research Center for Radiation Emergency Medicine, NIRS, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Prasanna, Pataje G.S. [National Cancer Institute, Division of Cancer Treatment and Diagnosis, Radiation Research Program, 6130 Executive Blvd., MSC 7440, Bethesda, MD 20892-7440 (United States)

    2011-09-15

    Biological dosimetry is an essential tool for estimating radiation doses received to personnel when physical dosimetry is not available or inadequate. The current preferred biodosimetry method is based on the measurement of radiation-specific dicentric chromosomes in exposed individuals' peripheral blood lymphocytes. However, this method is labor-, time- and expertise-demanding. Consequently, for mass casualty applications, strategies have been developed to increase its throughput. One such strategy is to develop validated cytogenetic biodosimetry laboratory networks, both national and international. In a previous study, the dicentric chromosome assay (DCA) was validated in our cytogenetic biodosimetry network involving five geographically dispersed laboratories. A complementary strategy to further enhance the throughput of the DCA among inter-laboratory networks is to use a triage DCA where dose assessments are made by truncating the labor-demanding and time-consuming metaphase spread analysis to 20 - 50 metaphase spreads instead of routine 500 - 1000 metaphase spread analysis. Our laboratory network also validated this triage DCA, however, these dose estimates were made using calibration curves generated in each laboratory from the blood samples irradiated in a single laboratory. In an emergency situation, dose estimates made using pre-existing calibration curves which may vary according to radiation type and dose rate and therefore influence the assessed dose. Here, we analyze the effect of using a pre-existing calibration curve on assessed dose among our network laboratories. The dose estimates were made by analyzing 1000 metaphase spreads as well as triage quality scoring and compared to actual physical doses applied to the samples for validation. The dose estimates in the laboratory partners were in good agreement with the applied physical doses and determined to be adequate for guidance in the treatment of acute radiation syndrome.

  12. Biological dosimetry of irradiation accidents

    International Nuclear Information System (INIS)

    Durand, V.; Chambrette, V.; Le Roy, A.; Paillole, N.; Sorokine, I.; Voisin, P.

    1994-01-01

    The biological dosimetry in radiation protection allows to evaluate the received dose by a potentially irradiated person from biological markers such chromosomal abnormalities. The technologies of Hybridization In Situ by Fluorescence (F.I.S.H) allow the detection of steady chromosomal aberrations of translocation type

  13. Calibration curves for biological dosimetry

    International Nuclear Information System (INIS)

    Guerrero C, C.; Brena V, M. . E-mail cgc@nuclear.inin.mx

    2004-01-01

    The generated information by the investigations in different laboratories of the world, included the ININ, in which settles down that certain class of chromosomal leisure it increases in function of the dose and radiation type, has given by result the obtaining of calibrated curves that are applied in the well-known technique as biological dosimetry. In this work is presented a summary of the work made in the laboratory that includes the calibrated curves for gamma radiation of 60 Cobalt and X rays of 250 k Vp, examples of presumed exposure to ionizing radiation, resolved by means of aberration analysis and the corresponding dose estimate through the equations of the respective curves and finally a comparison among the dose calculations in those people affected by the accident of Ciudad Juarez, carried out by the group of Oak Ridge, USA and those obtained in this laboratory. (Author)

  14. Development of radiation biological dosimetry

    International Nuclear Information System (INIS)

    Cho, Chul Koo; Kim, Tae Hwan; Lee, Yun Sil; Son, Young Sook; Kim, Soo Kwan; Jang, Won Suk; Le, Sun Joo; Jee, Young Heun; Jung, Woo Jung

    1999-04-01

    Up until now, only a few methods have been developed for radiation biological dosimetry such as conventional chromosome aberration and micronucleus in peripheral blood cell. However, because these methods not only can be estimated by the expert, but also have a little limitation due to need high technique and many times in the case of radiation accident, it is very difficult to evaluate the absorbed dose of victims. Therefore, we should develop effective, easy, simple and rapid biodosimetry and its guideline (triage) to be able to be treated the victims as fast as possible. We established the premature chromosome condensation assay and apoptotic fragment assay which was the significant relationship between dose and cell damages to evaluate the irradiation dose as correct and rapid as possible using lymphocytes and crypt cells, and compared with conventional chromosome aberration assay and micronuclei assay

  15. Development of radiation biological dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Chul Koo; Kim, Tae Hwan; Lee, Yun Sil; Son, Young Sook; Kim, Soo Kwan; Jang, Won Suk; Le, Sun Joo; Jee, Young Heun; Jung, Woo Jung

    1999-04-01

    Up until now, only a few methods have been developed for radiation biological dosimetry such as conventional chromosome aberration and micronucleus in peripheral blood cell. However, because these methods not only can be estimated by the expert, but also have a little limitation due to need high technique and many times in the case of radiation accident, it is very difficult to evaluate the absorbed dose of victims. Therefore, we should develop effective, easy, simple and rapid biodosimetry and its guideline (triage) to be able to be treated the victims as fast as possible. We established the premature chromosome condensation assay and apoptotic fragment assay which was the significant relationship between dose and cell damages to evaluate the irradiation dose as correct and rapid as possible using lymphocytes and crypt cells, and compared with conventional chromosome aberration assay and micronuclei assay.

  16. Realising the European network of bio-dosimetry (RENEB)

    International Nuclear Information System (INIS)

    Kulka, U.; Ainsbury, L.; Atkinson, M.; Barquinero, J. F.; Barrios, L.; Beinke, C.; Bognar, G.; Cucu, A.; Darroudi, F.; Fattibene, P.; Gil, O.; Gregoire, E.; Hadjidekova, V.; Haghdoost, S.; Herranz, R.; Jaworska, A.; Lindholm, C.; Mkacher, R.; Moertl, S.; Montoro, A.; Moquet, J.; Moreno, M.; Ogbazghi, A.; Oestreicher, U.; Palitti, F.; Pantelias, G.; Popescu, I.; Prieto, M. J.; Romm, H.; Rothkamm, K.; Sabatier, L.; Sommer, S.; Terzoudi, G.; Testa, A.; Thierens, H.; Trompier, F.; Turai, I.; Vandersickel, V.; Vaz, P.; Voisin, P.; Vral, A.; Ugletveit, F.; Woda, C.; Wojcik, A.

    2012-01-01

    In Europe, a network for biological dosimetry has been created to strengthen the emergency preparedness and response capabilities in case of a large-scale nuclear accident or radiological emergency. Through the RENEB (Realising the European Network of bio-dosimetry) project, 23 experienced laboratories from 16 European countries will establish a sustainable network for rapid, comprehensive and standardised bio-dosimetry provision that would be urgently required in an emergency situation on European ground. The foundation of the network is formed by five main pillars: (1) the ad hoc operational basis, (2) a basis of future developments, (3) an effective quality-management system, (4) arrangements to guarantee long-term sustainability and (5) awareness of the existence of RENEB. RENEB will thus provide a mechanism for quick, efficient and reliable support within the European radiation emergency management. The scientific basis of RENEB will concurrently contribute to increased safety in the field of radiation protection. (authors)

  17. Biological dosimetry, scopes and limitations

    International Nuclear Information System (INIS)

    Guerrero C, C.; Brena V, M.

    1999-01-01

    The analysis of the aberrations in chromosomes is an alternative to establish the exposure dose to the radiation, when the information provided by the traditional physical methods is insufficient. There are diverse causes by which it can reached to apply an alternative system, such is the case of exposures of another persons to the management of radiation sources, which not carry physical dosemeter. Contrary case is to the occupational exposure personnel (OEP), what must to utilize some system for determining the exposure dose, even so can be needed the case for more information. In any case, the cells from the affected person are the alternative without the biological system be overlap to the physical, it is complementary. (Author)

  18. DRDC Ottawa working standard for biological dosimetry

    International Nuclear Information System (INIS)

    Segura, T.M.; Prud'homme-Lalonde, L.; Thorleifson, E.; Lachapelle, S.; Mullins, D.; Qutob, S.; Wilkinson, D.

    2005-07-01

    This Standard provides quality assurance, quality control, and evaluation of the performance criteria for the purpose of accreditation of the Radiation Biology laboratory at Defence Research and Development Canada - Ottawa (DRDC Ottawa) using biological dosimetry to predict radiation exposure doses. The International Standard (ISO 19238) and the International Atomic Energy Association (IAEA) Technical Report Series No. 405 are used as guiding documents in preparation of this working document specific to the DRDC Ottawa Radiation Biology Laboratory. This Standard addresses: 1. The confidentiality of personal information, for the customer and the service laboratory; 2. The laboratory safety requirements; 3. The calibration sources and calibration dose ranges useful for establishing the reference dose-effect curves allowing the dose estimation from chromosome aberration frequency, and the minimum detection levels; 4. Transportation criteria for shipping of test samples to the laboratory; 5. Preparation of samples for analysis; 6. The scoring procedure for unstable chromosome aberrations used for biological dosimetry; 7. The criteria for converting a measured aberration frequency into an estimate of absorbed dose; 8. The reporting of results; 9. The quality assurance and quality control plan for the laboratory; and 10. Informative annexes containing examples of a questionnaire, instructions for customers, a data sheet for recording aberrations, a sample report and other supportive documents. (author)

  19. DRDC Ottawa working standard for biological dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Segura, T M; Prud' homme-Lalonde, L [Defence Research and Development Canada, Ottawa, Ontario (Canada); Thorleifson, E [Health Canada, Gatineau, Quebec (Canada); Lachapelle, S; Mullins, D [JERA Consulting (Canada); Qutob, S [Health Canada, Gatineau, Quebec (Canada); Wilkinson, D

    2005-07-15

    This Standard provides quality assurance, quality control, and evaluation of the performance criteria for the purpose of accreditation of the Radiation Biology laboratory at Defence Research and Development Canada - Ottawa (DRDC Ottawa) using biological dosimetry to predict radiation exposure doses. The International Standard (ISO 19238) and the International Atomic Energy Association (IAEA) Technical Report Series No. 405 are used as guiding documents in preparation of this working document specific to the DRDC Ottawa Radiation Biology Laboratory. This Standard addresses: 1. The confidentiality of personal information, for the customer and the service laboratory; 2. The laboratory safety requirements; 3. The calibration sources and calibration dose ranges useful for establishing the reference dose-effect curves allowing the dose estimation from chromosome aberration frequency, and the minimum detection levels; 4. Transportation criteria for shipping of test samples to the laboratory; 5. Preparation of samples for analysis; 6. The scoring procedure for unstable chromosome aberrations used for biological dosimetry; 7. The criteria for converting a measured aberration frequency into an estimate of absorbed dose; 8. The reporting of results; 9. The quality assurance and quality control plan for the laboratory; and 10. Informative annexes containing examples of a questionnaire, instructions for customers, a data sheet for recording aberrations, a sample report and other supportive documents. (author)

  20. Dosimetry and biological effects of fast neutrons

    International Nuclear Information System (INIS)

    Zoetelief, J.

    1981-01-01

    This thesis contains studies on two types of cellular damage: cell reproductive death and chromosome aberrations induced by irradiation with X rays, gamma rays and fast neutrons of different energies. A prerequisite for the performance of radiobiological experiments is the determination of the absorbed dose with a sufficient degree of accuracy and precision. Basic concepts of energy deposition by ionizing radiation and practical aspects of neutron dosimetry for biomedical purposes are discussed. Information on the relative neutron sensitivity of GM counters and on the effective point of measurement of ionization chambers for dosimetry of neutron and photon beams under free-in-air conditions and inside phantoms which are used to simulate the biological objects is presented. Different methods for neutron dosimetry are compared and the experimental techniques used for the investigations of cell reproductive death and chromosome aberrations induced by ionizing radiation of different qualities are presented. Dose-effect relations for induction cell inactivation and chromsome aberrations in three cultured cell lines for different radiation qualities are presented. (Auth.)

  1. The United Kingdom's radiotherapy dosimetry audit network

    International Nuclear Information System (INIS)

    Thwaites, D.I.; Allahverdi, M.; Powley, S.K.; Nisbet, A.

    2003-01-01

    The first comprehensive national dosimetry intercomparison in the United Kingdom involving all UK radiotherapy centres was carried out in the late 1980s. Out of this a regular radiotherapy dosimetry audit network evolved in the early 1990s. The network is co-ordinated by the Institute of Physics and Engineering in Medicine and comprises eight co-operative regional groups. Audits are based on site visits using ionization chambers and epoxy resin water substitute phantoms. The basic audit methodology and phantom design follows that of the original national intercomparison exercise. However, most of the groups have evolved more complex methods, to extend the audit scope to include other parameters, other parts of the radiotherapy process and other treatment modalities. A number of the groups have developed phantoms to simulate various clinical treatment situations, enabling the sharing of phantoms and expertise between groups, but retaining a common base. Besides megavoltage external beam photon dosimetry, a number of the groups have also included the audit of kilovoltage X ray beams, electron beams and brachytherapy dosimetry. The National Physical Laboratory is involved in the network and carries out basic beam calibration audits to link the groups. The network is described and the methods and results are illustrated using the Scottish+ group as an example. (author)

  2. About the factors distorting biological dosimetry results

    International Nuclear Information System (INIS)

    Mosseh, I.B.

    1999-01-01

    The row of chemical substances that have not mutagenic effect can strengthen ionising radiation induced cytogenetic effects. For example nitrite sodium and nitrate sodium reinforce mutagenic action of radiation and cause sensitized effect although they aren't mutagens. Presence of residual amount of herbicides in food products can have influence at level of aberration in human cells. It was investigated the influence of herbicide zencor at mutagenic action of radiation. This substance has weak mutagenic activity. In the case of combined action of zencor with irradiation antagonistic effect was observed. Mutation rate turns out to be lower than expected summary value. At the same time many foods products (tea, coffee, cacao, chocolate etc., which contain melanin) are antimutagens and can also change the frequency of radiation induced mutations. Taking of medicine distort the results of dose estimation. The frequency of chromosomal aberrations in blood lymphocytes after acute irradiation is considered to be adequate method of biological dosimetry. In the case of chronic irradiation this analysis becomes complicated with such processes as adaptation (selection and proliferation of cells with more radioresistant genotype) and the origin of genetic un stability which leads to higher radiosensitivity. The estimation of the level of point mutations is the most precise method of biological dosimetry because their existence is less exposed to modifications

  3. Dosimetry

    International Nuclear Information System (INIS)

    Rezende, D.A.O. de

    1976-01-01

    The fundamental units of dosimetry are defined, such as exposure rate, absorbed dose and equivalent dose. A table is given of relative biological effectiveness values for the different types of radiation. The relation between the roentgen and rad units is calculated and the concepts of physical half-life, biological half-life and effective half-life are discussed. Referring to internal dosimetry, a mathematical treatment is given to β particle-and γ radiation dosimetry. The absorbed dose is calculated and a practical example is given of the calculation of the exposure and of the dose rate for a gama source [pt

  4. Worldwide QA networks for radiotherapy dosimetry

    International Nuclear Information System (INIS)

    Izewska, J.; Svensson, H.; Ibbott, G.

    2002-01-01

    A number of national or international organizations have developed various types and levels of external audits for radiotherapy dosimetry. There are three major programmes who make available external audits, based on mailed TLD (thermoluminescent dosimetry), to local radiotherapy centres on a regular basis. These are the IAEA/WHO TLD postal dose audit service operating worldwide, the European Society for Therapeutic Radiology and Oncology (ESTRO) system, EQUAL, in European Union (EU) and the Radiological Physics Center (RPC) in North America. The IAEA, in collaboration with WHO, was the first organization to initiate TLD audits on an international scale in 1969, using mailed system, and has a well-established programme for providing dose verification in reference conditions. Over 32 years, the IAEA/WHO TLD audit service has checked the calibration of more than 4300 radiotherapy beams in about 1200 hospitals world-wide. Only 74% of those hospitals who receive TLDs for the first time have results with deviation between measured and stated dose within acceptance limits of ±5%, while approximately 88% of the users that have benefited from a previous TLD audit are successful. EQUAL, an audit programme set up in 1998 by ESTRO, involves the verification of output for high energy photon and electron beams, and the audit of beam parameters in non-reference conditions. More than 300 beams are checked each year, mainly in the countries of EU, covering approximately 500 hospitals. The results show that although 98% of the beam calibrations are within the tolerance level of ±5%, a second check was required in 10% of the participating centres, because a deviation larger than ±5% was observed in at least one of the beam parameters in non-reference conditions. EQUAL has been linked to another European network (EC network) which tested the audit methodology prior to its application. The RPC has been funded continuously since 1968 to monitor radiation therapy dose delivery at

  5. Cytogenetic biological dosimetry. Dose estimative in accidental exposure

    International Nuclear Information System (INIS)

    Santos, O.R. dos; Campos, I.M.A. de.

    1988-01-01

    The methodology of cytogenetic biological dosimetry is studied. The application in estimation of dose in five cases of accidental exposure is reported. An hematological study and culture of lymphocytes is presented. (M.A.C.) [pt

  6. Dosimetry

    International Nuclear Information System (INIS)

    Anon.

    1990-01-01

    The purpose of ionizing radiation dosimetry is the measurement of the physical and biological consequences of exposure to radiation. As these consequences are proportional to the local absorption of energy, the dosimetry of ionizing radiation is based on the measurement of this quantity. Owing to the size of the effects of ionizing radiation on materials in all of these area, dosimetry plays an essential role in the prevention and the control of radiation exposure. Its use is of great importance in two areas in particular where the employment of ionizing radiation relates to human health: radiation protection, and medical applications. Dosimetry is different for various reasons: owing to the diversity of the physical characteristics produced by different kinds of radiation according to their nature (X- and γ-photons, electrons, neutrons,...), their energy (from several keV to several MeV), the orders of magnitude of the doses being estimated (a factor of about 10 5 between diagnostic and therapeutic applications); and the temporal and spatial variation of the biological parameters entering into the calculations. On the practical level, dosimetry poses two distinct yet closely related problems: the determination of the absorbed dose received by a subject exposed to radiation from a source external to his body (external dosimetry); and the determination of the absorbed dose received by a subject owing to the presence within his body of some radioactive substance (internal dosimetry)

  7. The UK radiotherapy dosimetry audit network

    International Nuclear Information System (INIS)

    Thwaites, D.I.

    2002-01-01

    Full text: Radiotherapy dosimetry intercomparison in the UK has been carried out in limited studies since the 1960s. However the first national dosimetry intercomparison involving all radiotherapy centres was conducted in the late 1980s. This was based on visits to each centre, using ionisation chamber dosimetry. It audited megavoltage photon beam calibration and other single field parameters. It also measured doses in a three-field 'treatment' in a trapezoidal phantom constructed from epoxy-resin water-equivalent material and compared these to locally planned doses. This included off-axis points, oblique incidence, inhomogeneities, etc. The study found mean measured beam calibration doses close to stated values (ratio 1.003), with a standard deviation (sd) of the distribution of 1.5% and 97% of doses within the pro-set 3% tolerance. For the planned multi-field irradiations, mean dose ratios (measured/stated) were 1.01 (sd 3%, 90% of results within 5%). A number of discrepancies were identified, leading to improved practice. A follow up study (mid-1990s) for electron beam audit also repeated the megavoltage photon calibration audit. For photons, an improvement was noted (mean ratio 1.003, sd 1.0%, 100% within 3%), whilst for electron beams, the mean ratio of measured/stated dose was 0.994 (sd 1.8%, 94% within 3%, 99% within 5%). In parallel with - and growing out of - this, a national audit network began to develop in 1991/2. It utilised similar methodology to the intercomparison and a network approach to allow parallel developments of the scope of the system. The network has eight regional groups, each with up to 10 radiotherapy centres, serving average populations of 7-8 million. Each group organises audits of its own centres and has developed at its own pace. Most have piloted methodology, phantoms, etc. for new audits which can then be used by other groups. All 65 UK centres are included. The network is co-ordinated by an IPEM Steering Committee (current chair

  8. An IAEA Survey of Dosimetry Audit Networks for Radiotherapy

    International Nuclear Information System (INIS)

    Grochowska, Paulina; Izewska, Joanna

    2013-01-01

    A Survey: In 2010, the IAEA undertook a task to investigate and review the coverage and operations of national and international dosimetry audit programmes for radiotherapy. The aim was to organize the global database describing the activities of dosimetry audit networks in radiotherapy. A dosimetry audit questionnaire has been designed at an IAEA consultants' meeting held in 2010 for organizations conducting various levels of dosimetry audits for radiotherapy. Using this questionnaire, a survey was conducted for the first time in 2010 and repeated in 2011. Request for information on different aspects of the dosimetry audit was included, such as the audit framework and resources, its coverage and scope, the dosimetry system used and the modes of audit operation, i.e. remotely and through on-site visits. The IAEA questionnaire was sent to over 80 organizations, members of the IAEA/WHO Network of Secondary Standards Dosimetry Laboratories (SSDLs) and other organizations known for having operated dosimetry audits for radiotherapy in their countries or internationally. Survey results and discussion: In response to the IAEA survey, 53 organizations in 45 countries confirmed that they operate dosimetry audit services for radiotherapy. Mostly, audits are conducted nationally, however there are five organizations offering audits abroad, with two of them operating in various parts of the world and three of them at the regional level, auditing radiotherapy centres in neighbouring countries. The distribution of dosimetry audit services in the world is given. (author)

  9. Establishing working standards of chromosome aberrations analysis for biological dosimetry

    International Nuclear Information System (INIS)

    Bui Thi Kim Luyen; Tran Que; Pham Ngoc Duy; Nguyen Thi Kim Anh; Ha Thi Ngoc Lien

    2015-01-01

    Biological dosimetry is an dose assessment method using specify bio markers of radiation. IAEA (International Atomic Energy Agency) and ISO (International Organization for Standardization) defined that dicentric chromosome is specify for radiation, it is a gold standard for biodosimetry. Along with the documents published by IAEA, WHO, ISO and OECD, our results of study on the chromosome aberrations induced by radiation were organized systematically in nine standards that dealing with chromosome aberration test and micronucleus test in human peripheral blood lymphocytes in vitro. This standard addresses: the reference dose-effect for dose estimation, the minimum detection levels, cell culture, slide preparation, scoring procedure for chromosome aberrations use for biodosimetry, the criteria for converting aberration frequency into absorbed dose, reporting of results. Following these standards, the automatic analysis devices were calibrated for improving biological dosimetry method. This standard will be used to acquire and maintain accreditation of the Biological Dosimetry laboratory in Nuclear Research Institute. (author)

  10. Artificial neural networks in neutron dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Vega C, H.R.; Hernandez D, V.M.; Manzanares A, E.; Mercado, G.A.; Perales M, W.A.; Robles R, J.A. [Unidades Academicas de Estudios Nucleares, UAZ, A.P. 336, 98000 Zacatecas (Mexico); Gallego, E.; Lorente, A. [Depto. de Ingenieria Nuclear, Universidad Politecnica de Madrid, (Spain)

    2005-07-01

    An artificial neural network has been designed to obtain the neutron doses using only the Bonner spheres spectrometer's count rates. Ambient, personal and effective neutron doses were included. 187 neutron spectra were utilized to calculate the Bonner count rates and the neutron doses. The spectra were transformed from lethargy to energy distribution and were re-binned to 31 energy groups using the MCNP 4C code. Re-binned spectra, UTA4 response matrix and fluence-to-dose coefficients were used to calculate the count rates in Bonner spheres spectrometer and the doses. Count rates were used as input and the respective doses were used as output during neural network training. Training and testing was carried out in Mat lab environment. The artificial neural network performance was evaluated using the {chi}{sup 2}- test, where the original and calculated doses were compared. The use of Artificial Neural Networks in neutron dosimetry is an alternative procedure that overcomes the drawbacks associated in this ill-conditioned problem. (Author)

  11. Artificial neural networks in neutron dosimetry

    International Nuclear Information System (INIS)

    Vega C, H.R.; Hernandez D, V.M.; Manzanares A, E.; Mercado, G.A.; Perales M, W.A.; Robles R, J.A.; Gallego, E.; Lorente, A.

    2005-01-01

    An artificial neural network has been designed to obtain the neutron doses using only the Bonner spheres spectrometer's count rates. Ambient, personal and effective neutron doses were included. 187 neutron spectra were utilized to calculate the Bonner count rates and the neutron doses. The spectra were transformed from lethargy to energy distribution and were re-binned to 31 energy groups using the MCNP 4C code. Re-binned spectra, UTA4 response matrix and fluence-to-dose coefficients were used to calculate the count rates in Bonner spheres spectrometer and the doses. Count rates were used as input and the respective doses were used as output during neural network training. Training and testing was carried out in Mat lab environment. The artificial neural network performance was evaluated using the χ 2 - test, where the original and calculated doses were compared. The use of Artificial Neural Networks in neutron dosimetry is an alternative procedure that overcomes the drawbacks associated in this ill-conditioned problem. (Author)

  12. Artificial neural networks in neutron dosimetry

    International Nuclear Information System (INIS)

    Vega-Carrillo, H. R.; Hernandez-Davila, V. M.; Manzanares-Acuna, E.; Mercado, G. A.; Gallego, E.; Lorente, A.; Perales-Munoz, W. A.; Robles-Rodriguez, J. A.

    2006-01-01

    An artificial neural network (ANN) has been designed to obtain neutron doses using only the count rates of a Bonner spheres spectrometer (BSS). Ambient, personal and effective neutron doses were included. One hundred and eighty-one neutron spectra were utilised to calculate the Bonner count rates and the neutron doses. The spectra were transformed from lethargy to energy distribution and were re-binned to 31 energy groups using the MCNP 4C code. Re-binned spectra, UTA4 response matrix and fluence-to-dose coefficients were used to calculate the count rates in the BSS and the doses. Count rates were used as input and the respective doses were used as output during neural network training. Training and testing were carried out in the MATLAB R environment. The impact of uncertainties in BSS count rates upon the dose quantities calculated with the ANN was investigated by modifying by ±5% the BSS count rates used in the training set. The use of ANNs in neutron dosimetry is an alternative procedure that overcomes the drawbacks associated with this ill-conditioned problem. (authors)

  13. Synthetic biological networks

    International Nuclear Information System (INIS)

    Archer, Eric; Süel, Gürol M

    2013-01-01

    Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

  14. Networks in Cell Biology

    Science.gov (United States)

    Buchanan, Mark; Caldarelli, Guido; De Los Rios, Paolo; Rao, Francesco; Vendruscolo, Michele

    2010-05-01

    Introduction; 1. Network views of the cell Paolo De Los Rios and Michele Vendruscolo; 2. Transcriptional regulatory networks Sarath Chandra Janga and M. Madan Babu; 3. Transcription factors and gene regulatory networks Matteo Brilli, Elissa Calistri and Pietro Lió; 4. Experimental methods for protein interaction identification Peter Uetz, Björn Titz, Seesandra V. Rajagopala and Gerard Cagney; 5. Modeling protein interaction networks Francesco Rao; 6. Dynamics and evolution of metabolic networks Daniel Segré; 7. Hierarchical modularity in biological networks: the case of metabolic networks Erzsébet Ravasz Regan; 8. Signalling networks Gian Paolo Rossini; Appendix 1. Complex networks: from local to global properties D. Garlaschelli and G. Caldarelli; Appendix 2. Modelling the local structure of networks D. Garlaschelli and G. Caldarelli; Appendix 3. Higher-order topological properties S. Ahnert, T. Fink and G. Caldarelli; Appendix 4. Elementary mathematical concepts A. Gabrielli and G. Caldarelli; References.

  15. Dominating biological networks.

    Directory of Open Access Journals (Sweden)

    Tijana Milenković

    Full Text Available Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of "biologically central (BC" genes (i.e., their protein products, such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network.To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its "spine" that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks.

  16. Study on biological dosimetry of premature chromosome condensation technique

    International Nuclear Information System (INIS)

    Jiang Bo

    2005-01-01

    The premature chromosome condensation technique has been applied for biological dosimetry purpose. Premature chromo-some condensation was induced by incubating unstimulated human peripheral blood lymphocytes in the presence of okadaic acid or calyculin A (a phosphatase inhibitor) which eliminated the need for fusion with mitotic cells. It is now possible to examine the early damage induced by radiation. It is simple, exact when it combines with fluorecence in situ hybridization. (authors)

  17. Overview of physical dosimetry methods for triage application integrated in the new European network RENEB.

    Science.gov (United States)

    Trompier, François; Burbidge, Christopher; Bassinet, Céline; Baumann, Marion; Bortolin, Emanuela; De Angelis, Cinzia; Eakins, Jonathan; Della Monaca, Sara; Fattibene, Paola; Quattrini, Maria Cristina; Tanner, Rick; Wieser, Albrecht; Woda, Clemens

    2017-01-01

    In the EC-funded project RENEB (Realizing the European Network in Biodosimetry), physical methods applied to fortuitous dosimetric materials are used to complement biological dosimetry, to increase dose assessment capacity for large-scale radiation/nuclear accidents. This paper describes the work performed to implement Optically Stimulated Luminescence (OSL) and Electron Paramagnetic Resonance (EPR) dosimetry techniques. OSL is applied to electronic components and EPR to touch-screen glass from mobile phones. To implement these new approaches, several blind tests and inter-laboratory comparisons (ILC) were organized for each assay. OSL systems have shown good performances. EPR systems also show good performance in controlled conditions, but ILC have also demonstrated that post-irradiation exposure to sunlight increases the complexity of the EPR signal analysis. Physically-based dosimetry techniques present high capacity, new possibilities for accident dosimetry, especially in the case of large-scale events. Some of the techniques applied can be considered as operational (e.g. OSL on Surface Mounting Devices [SMD]) and provide a large increase of measurement capacity for existing networks. Other techniques and devices currently undergoing validation or development in Europe could lead to considerable increases in the capacity of the RENEB accident dosimetry network.

  18. Activities developed by the biological dosimetry laboratory of the Autoridad Regulatoria Nuclear - ARN of Argentina

    International Nuclear Information System (INIS)

    Radl, A.; Sapienza, C.E.; Taja, M.R.; Bubniak, R.; Deminge, M.; Di Giorgio, M.

    2013-01-01

    Biological dosimetry (DB) allows to estimate doses absorbed in individuals exposed to ionizing radiation through the quantification of stable and unstable chromosome aberrations (SCA and UCA). The frequency of these aberrations is referred to a calibration dose response curve (in vitro) to determine the doses of the individual to the whole body. The DB is a necessary support for programs of national radiation protection and response systems in nuclear or radiological emergencies in the event of accidental or incidental, single overexposure or large scale. In this context the Laboratory of Dosimetry Biological (LDB) of the Authority Regulatory Nuclear (ARN) Argentina develops and applies different dosimeters cytogenetic from four decades ago. These dosimeters provide a fact more within the whole of the information necessary for an accidental, complementing the physical and clinical dosimetry exposure assessment. The most widely used in the DB biodosimetric method is the quantification of SCA (dicentrics and rings Central) from a sample of venous blood. The LDB is accredited for the trial, under rules IRAM 301: 2005 (ISO / IEC 17025: 2005) and ISO 19238:2004. Test applies to the immediate dosimetry evaluation of acute exposures, all or a large part of the body in the range 0,1-5 Gy. In this context the LDB is part of the Latin American network of DB (LBDNet), BioDoseNet-who and response system in radiological emergencies and nuclear IAEA-RANET, being enabled to summon the LBDNet if necessary

  19. Direct biological dosimetry in Chernobyl clear-up workers

    International Nuclear Information System (INIS)

    Maznik, N.A.; Vinnikov, V.A.; Rozdil'ski, S.I.

    1999-01-01

    Full text: In cases of large-scale radiological accidents like Chernobyl (1986) the estimation of somatic risk to exposed populations became a problem due to lack of direct physical dosimetry data. In such conditions the necessarily information can be obtained from biological dosimetry, firstly by chromosomal aberrations analysis in human peripheral blood lymphocytes. Conventional cytogenetic assay have been carried out in 130 persons recruited as clean-up workers ('liquidators') to the Chernobyl zone in 1986-87 yrs. Blood sampling was performed during 1 year post-irradiation, in 100 persons p to 0.5 year. The aberrations of choice for biological dosimetry were unstable chromosome exchanges (dicentrics and centric rings with accompanying acentric fragments). The dose calculations have been done using the linear term of the dose-response curve built with acute gamma-irradiation of blood in dose range up to 1 Gy. The distributions of biological doses were investigated in groups of liquidators with doses in documents ranging 17-140, 175-230, 250, 260-365, 440-1030 mSv and in the group of non-monitored persons. The weak correlation between monitored individual doses and biological doses was shown; the biological and physical dose distribution peculiarity in monitored groups is discussed. The distribution of individual aberration frequencies and the average yield of chromosomal exchanges in monitored and non-monitored liquidators were identical. The common cohort analysis (monitored and non-monitored persons) showed that the individual aberration yields distribution among liquidators was strictly randomised in accordance with Poissonian statistics. The cytogenetic dose estimations obtained can be of great value for somatic effects risk assessment in post-Chernobyl cohorts

  20. Role of cytogenetic techniques in biological dosimetry of absorbed radiation

    International Nuclear Information System (INIS)

    Rao, B.S.

    2016-01-01

    In most of the radiation accidents, physical dosimetric information is rarely available. Further, most of the accidental exposures are non-uniform involving either partial body or localized exposure to significant doses. In such situations, physical dosimetry does not provide reliable dose estimate. It has now been realized that biological dosimetric techniques can play an important role in the assessment of absorbed dose. In recent years, a number of biological indicators of radiation have been identified. These include the kinetics of onset and persistence of prodromal syndromes (radiation sickness), cytogenetic changes in peripheral blood lymphocytes, hematological changes, biochemical indicators, ESR spectroscopy of biological samples, induction of gene mutations in red blood cells, cytogenetic and physiological changes in skin and neurophysiological changes. In general, dosimetric information is derived by a combination of several different methods, as they have potential to serve as prognostic indicators. The role of cytogenetic techniques in peripheral blood lymphocytes (PBL) as biological indicators of absorbed radiation is reviewed here

  1. Chromosome aberration analysis for biological dosimetry: a review

    International Nuclear Information System (INIS)

    Paul, S.F.D.; Venkatachalam, P.; Jeevanram, R.K.

    1996-01-01

    Among various biological dosimetry techniques, dicentric chromosome aberration method appears to be the method of choice in analysing accidental radiation exposure in most of the laboratories. The major advantage of this method is its sensitivity as the number of dicentric chromosomes present in control population is too small and more importantly radiation induces mainly dicentric chromosome aberration among unstable aberration. This report brings out the historical development of various cytogenetic methods, the basic structure of DNA, chromosomes and different forms of chromosome aberrations. It also highlights the construction of dose-response curve for dicentric chromosome and its use in the estimation of radiation dose. (author)

  2. Biological dosimetry: chromosomal aberration analysis for dose assessment

    International Nuclear Information System (INIS)

    1986-01-01

    In view of the growing importance of chromosomal aberration analysis as a biological dosimeter, the present report provides a concise summary of the scientific background of the subject and a comprehensive source of information at the technical level. After a review of the basic principles of radiation dosimetry and radiation biology basic information on the biology of lymphocytes, the structure of chromosomes and the classification of chromosomal aberrations are presented. This is followed by a presentation of techniques for collecting blood, storing, transporting, culturing, making chromosomal preparations and scaring of aberrations. The physical and statistical parameters involved in dose assessment are discussed and examples of actual dose assessments taken from the scientific literature are given

  3. Metabolomics in Radiation-Induced Biological Dosimetry: A Mini-Review and a Polyamine Study

    Directory of Open Access Journals (Sweden)

    Changhyun Roh

    2018-05-01

    Full Text Available In this study, we elucidate that polyamine metabolite is a powerful biomarker to study post-radiation changes. Metabolomics in radiation biodosimetry, the application of a metabolomics analysis to the field of radiobiology, promises to increase the understanding of biological responses by ionizing radiation (IR. Radiation exposure triggers a complex network of molecular and cellular responses that impacts metabolic processes and alters the levels of metabolites. Such metabolites have potential as biomarkers for radiation dosimetry. Among metabolites, polyamine is one of many potential biomarkers to estimate radiation response. In addition, this review provides an opportunity for the understanding of a radiation metabolomics in biodosimetry and a polyamine case study.

  4. Biological dosimetry of X-rays by micronuclei study

    International Nuclear Information System (INIS)

    Gomez, E.; Silva, A.; Navlet, J.

    1991-01-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in hematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes cytokinetic blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y=c+ α D+β D 2 where. Y is the number micronuclei per cell and D the dose. the curve is compared with those produced elsewhere

  5. Biological Dosimetry of X-rays by micronuclei study

    International Nuclear Information System (INIS)

    Gomez, E.; Silva, A.; Navlet, J.

    1991-01-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes citokinetics blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree centigree has been produced. Experimental data is fitted to model Y=C+ αD+BD''2 where Y is the number of micronuclei per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 24 refs

  6. Biological dosimetry of ionizing radiation by chromosomal aberration analysis

    International Nuclear Information System (INIS)

    Gonzalez-Castano, S.; Silva, A.; Navlet, J.

    1990-01-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical, and cytogenetic data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable. In this case, the study ol chromosomal aberrations, normally dicentric chromosomes, in peripheral lymphocytes can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using dicentric chromosomes analysis, X-rays at 300 kVp, 114 rad/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y =α + β 1 D + β 2 D 2 , where Y is the number of dicentrics per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 14 refs

  7. Biological dosimetry of ionizing radiation by chromosomal aberration analysis

    International Nuclear Information System (INIS)

    Navlet Armenta, J.M.; Gonzalez, S.; Silva, A.

    1990-01-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haemathological, biochemical, and cytogenetic data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable. In this case, the study of chromosomal aberrations, normally dicentric chromosomes, in peripheral lymphocytes can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve using dicentric chromosomes analysis, X-rays at 300 kVp, 114 rad/min and temperature 37 o C has been produced. Experimental data is fitted to model Y = α+β 1 D+β 2 D 2 , where Y is the number of dicentrics per cell and D the dose. The curve is compared with those produced elsewhere. (Author)

  8. The method validation step of biological dosimetry accreditation process

    International Nuclear Information System (INIS)

    Roy, L.; Voisin, P.A.; Guillou, A.C.; Busset, A.; Gregoire, E.; Buard, V.; Delbos, M.; Voisin, Ph.

    2006-01-01

    One of the missions of the Laboratory of Biological Dosimetry (L.D.B.) of the Institute for Radiation and Nuclear Safety (I.R.S.N.) is to assess the radiological dose after an accidental overexposure suspicion to ionising radiation, by using radio-induced changes of some biological parameters. The 'gold standard' is the yield of dicentrics observed in patients lymphocytes, and this yield is converted in dose using dose effect relationships. This method is complementary to clinical and physical dosimetry, for medical team in charge of the patients. To obtain a formal recognition of its operational activity, the laboratory decided three years ago, to require an accreditation, by following the recommendations of both 17025 General Requirements for the Competence of Testing and Calibration Laboratories and 19238 Performance criteria for service laboratories performing biological dosimetry by cyto-genetics. Diagnostics, risks analysis were realized to control the whole analysis process leading to documents writing. Purchases, personnel department, vocational training were also included in the quality system. Audits were very helpful to improve the quality system. One specificity of this technique is that it is not normalized therefore apart from quality management aspects, several technical points needed some validations. An inventory of potentially influent factors was carried out. To estimate their real effect on the yield of dicentrics, a Placket-Burman experimental design was conducted. The effect of seven parameters was tested: the BUdr (bromodeoxyuridine), PHA (phytohemagglutinin) and colcemid concentration, the culture duration, the incubator temperature, the blood volume and the medium volume. The chosen values were calculated according to the uncertainties on the way they were measured i.e. pipettes, thermometers, test tubes. None of the factors has a significant impact on the yield of dicentrics. Therefore the uncertainty linked to their use was considered as

  9. The method validation step of biological dosimetry accreditation process

    Energy Technology Data Exchange (ETDEWEB)

    Roy, L.; Voisin, P.A.; Guillou, A.C.; Busset, A.; Gregoire, E.; Buard, V.; Delbos, M.; Voisin, Ph. [Institut de Radioprotection et de Surete Nucleaire, LDB, 92 - Fontenay aux Roses (France)

    2006-07-01

    One of the missions of the Laboratory of Biological Dosimetry (L.D.B.) of the Institute for Radiation and Nuclear Safety (I.R.S.N.) is to assess the radiological dose after an accidental overexposure suspicion to ionising radiation, by using radio-induced changes of some biological parameters. The 'gold standard' is the yield of dicentrics observed in patients lymphocytes, and this yield is converted in dose using dose effect relationships. This method is complementary to clinical and physical dosimetry, for medical team in charge of the patients. To obtain a formal recognition of its operational activity, the laboratory decided three years ago, to require an accreditation, by following the recommendations of both 17025 General Requirements for the Competence of Testing and Calibration Laboratories and 19238 Performance criteria for service laboratories performing biological dosimetry by cyto-genetics. Diagnostics, risks analysis were realized to control the whole analysis process leading to documents writing. Purchases, personnel department, vocational training were also included in the quality system. Audits were very helpful to improve the quality system. One specificity of this technique is that it is not normalized therefore apart from quality management aspects, several technical points needed some validations. An inventory of potentially influent factors was carried out. To estimate their real effect on the yield of dicentrics, a Placket-Burman experimental design was conducted. The effect of seven parameters was tested: the BUdr (bromodeoxyuridine), PHA (phytohemagglutinin) and colcemid concentration, the culture duration, the incubator temperature, the blood volume and the medium volume. The chosen values were calculated according to the uncertainties on the way they were measured i.e. pipettes, thermometers, test tubes. None of the factors has a significant impact on the yield of dicentrics. Therefore the uncertainty linked to their use was

  10. Probabilistic biological network alignment.

    Science.gov (United States)

    Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2013-01-01

    Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

  11. Non-invasive biological dosimetry of the skin

    International Nuclear Information System (INIS)

    Barton, S.; Marks, R.; Charles, M.W.; Wells, J.

    1986-01-01

    Investigations designed to identify a potential biological dosimetry technique to examine the effects of X-ray doses down to 0.1 Gy on human skin, are described. In a variety of parameters assessed, the most important changes observed were a significant depression in epidermal cell production in the basal layer after X-ray doses between 0.5 Gy and 1 Gy and a concomitant reduction in the desquamation rate of corneocytes after doses above 1 Gy. Changes in non-specific esterase (NSE) activity were also observed. Further work is described which applies these results to several non-invasive techniques which may have potential for routine application. Preliminary data from irradiated human skin are presented on the measurement of forced desquamation, the evaluation of NSE activity from hair samples and the evaluation of stratum corneum turnover time using the fluorescent dye, dansyl chloride. (author)

  12. New methodologies of biological dosimetry applied to human protection

    International Nuclear Information System (INIS)

    Catena, C.; Parasacchi, P.; Conti, D.; Righi, E.

    1995-04-01

    Biological dosimetry is a diagnostic methodology for the measurement of the individual dose absorbed in the case of accidental overexposition to ionizing radiation. It is demonstrated how in vitro radiobiological and chemobiological studies using cytogenetic methods (count of chromosomal aberrations and micronuclei) on human lymphocytes from healthy subjects and individuals undergoing radiotherapy or chemotherapy, as well as on lymphocytes of mammals other than man (comparative cytogenetics), can help to increase the basic radiobiological and chemobiological scientific information. Such information gives a valid contribution to understanding of the action of ionizing radiation or of pharmaceuticals on cells and, in return, can be of value to human radioprotection and chemoprotection. Cytogenetic studies can be summerized as follows: a) biodosimetry (estimate of dose received after accidental events); b) individual radiosensitivity (level of individual response); c) clinical radiobiology and chemobiology (individual response to radiopharmaceuticals, to radiotherapy and to chemopharmaceuticals); d) comparative radiobiology (cytogenetic studies on species other than man); e) animal model in the environmental surveillance

  13. Calibration Curves for Biological Dosimetry by Fluorescence In situ Hybridisation

    International Nuclear Information System (INIS)

    Stonati, L.; Durante, M.; Gensabella, G.; Gialanella, G.; Grossi, G.F.; Pugliese, M.; Scampoli, P.; Sgura, A.; Testa, A.; Tanzarella, C.

    2001-01-01

    Dose-response curves were measured for the induction of chromosomal aberrations in peripheral blood lymphocytes after acute exposure in vitro to 60 Co γ rays. Blood was obtained from four different healthy donors, and chromosomes were either observed at metaphase, following colcemid accumulation, or prematurely condensed by calyculin A. Cells were analysed in three different Italian laboratories. Chromosomes 1, 2, and 4 were painted, and simple-type interchanges between painted and non-painted chromosomes were scored in cells exposed in the dose range 0.1-3.0 Gy. The chemical-induced premature chromosome condensation method was also used combined with chromosome painting (chromosome 4 only) to determine calibration curves for high dose exposures (up to 20 Gy X rays). Calibration curves described in this paper will be used in our laboratories for biological dosimetry by fluorescence in situ hybridisation. (author)

  14. Biological dosimetry for mixed gamma-neutron field

    International Nuclear Information System (INIS)

    Brandao, J.O.C.; Santos, J.A.L.; Souza, P.L.G.; Lima, F.F.; Vilela, E.C.; Calixto, M.S.; Santos, N.

    2011-01-01

    There is increasing concern about airline crew members (about one million worldwide) exposed to measurable neutrons doses. Historically, cytogenetic biodosimetry assays have been based on quantifying asymmetrical chromosome alterations (dicentrics, centric rings and acentric fragments) in mitogen-stimulated T-lymphocytes in their first mitosis after radiation exposure. Increased levels of chromosome damage in peripheral blood lymphocytes are a sensitive indicator of radiation exposure and they are routinely exploited for assessing radiation absorbed dose after accidental or occupational exposure. Since radiological accidents are not common, not all nations feel that it is economically justified to maintain biodosimetry competence. However, dependable access to biological dosimetry capabilities is completely critical in event of an accident. In this paper the dose-response curve was measured for the induction of chromosomal alterations in peripheral blood lymphocytes after chronic exposure in vitro to mixed gamma-neutron field. Blood was obtained from one healthy donor and exposed to two mixed gamma-neutron field from sources 241 AmBe (20 Ci) at the Neutron Calibration Laboratory (NCL - CRCN/NE - PE - Brazil). The evaluated absorbed doses were 0.2 Gy; 1.0 Gy and 2.5 Gy. The dicentric chromosomes were observed at metaphase, following colcemide accumulation and 1000 well-spread metaphases were analyzed for the presence of dicentrics by two experts after painted by giemsa 5%. The preliminary results showed a linear dependence between radiations absorbed dose and dicentric chromosomes frequencies. Dose-response curve described in this paper will contribute to the construction of calibration curve that will be used in our laboratory for biological dosimetry. (author)

  15. Developments in biological dosimetry for the nuclear industry

    Energy Technology Data Exchange (ETDEWEB)

    Gale, K L; Boreham, D R; Maves, S; Morrison, D P [Atomic Energy of Canada Ltd., Chalk River, ON (Canada)

    1996-12-31

    The purpose of this program is to develop methods for providing estimates of radiation exposure based on changes in the cells/tissues of exposed individuals. This work arises from the need for independent measures of exposure of workers when standard dose measurements are unavailable or questionable. The radiation-induced changes that we propose to measure have been correlated with carcinogenesis. It follows that the methods used should also provide indications of the likely biological consequences of radiation exposure for an individual. The consequences of radiation exposure lie in the resolution of the radiation effects at the cellular level. Accordingly, it is at the cellular level that our attention is directed. More precisely, since the consequences of most concern, cancer induction and the induction of inherited diseases, are the result of changes to the genetic material of cells (the DNA), it is the measurement of effects on DNA that are being investigated as possible dose meters. Individuals are unique in terms of their DNA and differ in their cellular capacities to repair the damage from an ionizing radiation dose. Because of these features, not only do biological dosimetry tools offer us a means of measuring a dose at the individual level but may also provide us with a measure of the ultimate risk associated with a given exposure. (author). 7 refs., 2 tabs., 4 figs.

  16. Developments in biological dosimetry for the nuclear industry

    International Nuclear Information System (INIS)

    Gale, K.L.; Boreham, D.R.; Maves, S.; Morrison, D.P.

    1995-01-01

    The purpose of this program is to develop methods for providing estimates of radiation exposure based on changes in the cells/tissues of exposed individuals. This work arises from the need for independent measures of exposure of workers when standard dose measurements are unavailable or questionable. The radiation-induced changes that we propose to measure have been correlated with carcinogenesis. It follows that the methods used should also provide indications of the likely biological consequences of radiation exposure for an individual. The consequences of radiation exposure lie in the resolution of the radiation effects at the cellular level. Accordingly, it is at the cellular level that our attention is directed. More precisely, since the consequences of most concern, cancer induction and the induction of inherited diseases, are the result of changes to the genetic material of cells (the DNA), it is the measurement of effects on DNA that are being investigated as possible dose meters. Individuals are unique in terms of their DNA and differ in their cellular capacities to repair the damage from an ionizing radiation dose. Because of these features, not only do biological dosimetry tools offer us a means of measuring a dose at the individual level but may also provide us with a measure of the ultimate risk associated with a given exposure. (author). 7 refs., 2 tabs., 4 figs

  17. Statistical issues in biological radiation dosimetry for risk assessment using stable chromosome aberrations

    International Nuclear Information System (INIS)

    Cologne, J.B.; Preston, D.L.

    1998-01-01

    Biological dosimeters are useful for epidemiologic risk assessment in populations exposed to catastrophic nuclear events and as a means of validating physical dosimetry in radiation workers. Application requires knowledge of the magnitude of uncertainty in the biological dose estimates and an understanding of potential statistical pitfalls arising from their use. This paper describes the statistical aspects of biological dosimetry in general and presents a detailed analysis in the specific case of dosimetry for risk assessment using stable chromosome aberration frequency. Biological dose estimates may be obtained from a dose-response curve, but negative estimates can result and adjustment must be made for regression bias due to imprecise estimation when the estimates are used in regression analyses. Posterior-mean estimates, derived as the mean of the distribution of true doses compatible with a given value of the biological endpoint, have several desirable properties: they are nonnegative, less sensitive to extreme skewness in the true dose distribution, and implicitly adjusted to avoid regression bias. The methods necessitate approximating the true-dose distribution in the population in which biological dosimetry is being applied, which calls for careful consideration of this distribution through other information. An important question addressed here is to what extent the methods are robust to misspecification of this distribution, because in many applications of biological dosimetry it cannot be characterized well. The findings suggest that dosimetry based solely on stable chromosome aberration frequency may be useful for population-based risk assessment

  18. Usefulness and limits of biological dosimetry based on cytogenetic methods

    International Nuclear Information System (INIS)

    Leonard, A.; Rueff, J.; Gerber, G. B.; Leonard, E. D.

    2005-01-01

    Damage from occupational or accidental exposure to ionising radiation is often assessed by monitoring chromosome aberrations in peripheral blood lymphocytes, and these procedures have, in several cases, assisted physicians in the management of irradiated persons. Thereby, circulating lymphocytes, which are in the G0 stage of the cell cycle are stimulated with a mitogenic agent, usually phytohaemagglutinin, to replicate in vitro their DNA and enter cell division, and are then observed for abnormalities. Comparison with dose response relationships obtained in vitro allows an estimate of exposure based on scoring: - Unstable aberrations by the conventional, well-established analysis of metaphases for chromosome abnormalities or for micronuclei; - So-called stable aberrations by the classical G-banding (Giemsa-Stain-banding) technique or by the more recently developed fluorescent in situ hybridisation (FISH) method using fluorescent-labelled probes for centromeres and chromosomes. Three factors need to be considered in applying such biological dosimetry: (1) Radiation doses in the body are often inhomogeneous. A comparison of the distribution of the observed aberrations among with that expected from a normal poisson distribution can allow conclusions to be made with regard to the inhomogeneity of exposure by means of the so-called contaminated poisson distribution method; however, its application requires a sufficiently large number of aberrations, i.e. an exposure to a rather large dose at a high dose rate. (2) Exposure can occur at a low dose rate (e.g. from spread or lost radioactive sources) rendering a comparison with in vitro exposure hazardous. Dose-effect relationships of most aberrations that were scored, such as translocations, follow a square law. Repair intervening during exposure reduces the quadratic component with decreasing dose rate as exposure is spread over a longer period of time. No valid solution for this problem has yet been developed, although

  19. Querying Large Biological Network Datasets

    Science.gov (United States)

    Gulsoy, Gunhan

    2013-01-01

    New experimental methods has resulted in increasing amount of genetic interaction data to be generated every day. Biological networks are used to store genetic interaction data gathered. Increasing amount of data available requires fast large scale analysis methods. Therefore, we address the problem of querying large biological network datasets.…

  20. Neutron spectrometry and dosimetry by means of evolutive neural networks

    International Nuclear Information System (INIS)

    Ortiz R, J.M.; Martinez B, M.R.; Vega C, H.R.

    2008-01-01

    The artificial neural networks and the genetic algorithms are two relatively new areas of research, which have been subject to a growing interest during the last years. Both models are inspired by the nature, however, the neural networks are interested in the learning of a single individual, which is defined as fenotypic learning, while the evolutionary algorithms are interested in the adaptation of a population to a changing environment, that which is defined as genotypic learning. Recently, the use of the technology of neural networks has been applied with success in the area of the nuclear sciences, mainly in the areas of neutron spectrometry and dosimetry. The structure (network topology), as well as the learning parameters of a neural network, are factors that contribute in a significant way with the acting of the same one, however, it has been observed that the investigators in this area, carry out the selection of the network parameters through the essay and error technique, that which produces neural networks of poor performance and low generalization capacity. From the revised sources, it has been observed that the use of the evolutionary algorithms, seen as search techniques, it has allowed him to be possible to evolve and to optimize different properties of the neural networks, just as the initialization of the synaptic weights, the network architecture or the training algorithms without the human intervention. The objective of the present work is focused in analyzing the intersection of the neural networks and the evolutionary algorithms, analyzing like it is that the same ones can be used to help in the design processes and training of a neural network, this is, in the good selection of the structural parameters and of network learning, improving its generalization capacity, in such way that the same one is able to reconstruct in an efficient way neutron spectra and to calculate equivalent doses starting from the counting rates of a Bonner sphere

  1. Modular analysis of biological networks.

    Science.gov (United States)

    Kaltenbach, Hans-Michael; Stelling, Jörg

    2012-01-01

    The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.

  2. Training of reverse propagation neural networks applied to neutron dosimetry

    International Nuclear Information System (INIS)

    Hernandez P, C. F.; Martinez B, M. R.; Leon P, A. A.; Espinoza G, J. G.; Castaneda M, V. H.; Solis S, L. O.; Castaneda M, R.; Ortiz R, M.; Vega C, H. R.; Mendez V, R.; Gallego, E.; De Sousa L, M. A.

    2016-10-01

    Neutron dosimetry is of great importance in radiation protection as aims to provide dosimetric quantities to assess the magnitude of detrimental health effects due to exposure of neutron radiation. To quantify detriment to health is necessary to evaluate the dose received by the occupationally exposed personnel using different detection systems called dosimeters, which have very dependent responses to the energy distribution of neutrons. The neutron detection is a much more complex problem than the detection of charged particles, since it does not carry an electric charge, does not cause direct ionization and has a greater penetration power giving the possibility of interacting with matter in a different way. Because of this, various neutron detection systems have been developed, among which the Bonner spheres spectrometric system stands out due to the advantages that possesses, such as a wide range of energy, high sensitivity and easy operation. However, once obtained the counting rates, the problem lies in the neutron spectrum deconvolution, necessary for the calculation of the doses, using different mathematical methods such as Monte Carlo, maximum entropy, iterative methods among others, which present various difficulties that have motivated the development of new technologies. Nowadays, methods based on artificial intelligence technologies are being used to perform neutron dosimetry, mainly using the theory of artificial neural networks. In these new methods the need for spectrum reconstruction can be eliminated for the calculation of the doses. In this work an artificial neural network or reverse propagation was trained for the calculation of 15 equivalent doses from the counting rates of the Bonner spheres spectrometric system using a set of 7 spheres, one of 2 spheres and two of a single sphere of different sizes, testing different error values until finding the most appropriate. The optimum network topology was obtained through the robust design

  3. An improved in vitro micronucleus assay to biological dosimetry

    International Nuclear Information System (INIS)

    Ocampo, Ivette Z.; Okazaki, Kayo; Vieira, Daniel P.

    2013-01-01

    The biological dosimetry is widely used to estimate the absorbed dose in people occupationally or accidentally exposed to the radiation for a better medical treatment, minimizing the harmful effects. Many techniques and methods have been proposed to detect and quantify the radioinduced lesions in genetic material, among them, the micronucleus (MN) assay. In the present study, we proposed an improved in vitro micronucleus technique that is rapid, sensitive and with minor cell manipulations. Assays were carried out with human tumor cells (MCF-7) seeded (3x10 4 cells) in slides placed into Petri dishes. Adherent cells were maintained with RPMI medium, supplemented with fetal calf serum, 1 % antibiotics, cytochalasin B (2 μg/mL), and incubated at 37 deg C in the presence of 5% CO2 for 72h. Cells were pre-treated for 24h with aminoguanidine, a nitric oxide synthase inhibitor. Nitric oxide is an intracellular free-radical, involved in DNA double-strand break repair mechanisms. After incubation, adherent cells on slides were briefly fixed with paraformaldehyde and stained with acridine orange (100 μg/mL) for analysis through fluorescence microscopy. Dye fluorescence permitted accurate discrimination between nuclei and micronuclei (bright green) and cytoplasm (red), and made possible a faster counting of binucleated cells. Aminoguanidine (2 mM) induced significant increase (p< 0.05) in frequencies of binucleated cells with micronuclei and in the number of micronuclei per binucleated cell. Data showed that proposed modifications permit to understand an early aspect of NO inhibition and suggested an improved protocol to MN assays. (author)

  4. The IAEA/WHO network of Secondary Standard Dosimetry Laboratories. SSDL network charter

    International Nuclear Information System (INIS)

    1999-04-01

    In 1976, the International Atomic Energy Agency (IAEA) together with the World Health Organization (WHO) established a Network of Secondary Standard Dosimetry Laboratories (SSDLs), known as the IAEA/WHO SSDL Network. This Network, through SSDLs designated by Member States, provides a direct linkage of national dosimetry standards to the international measurement system of standards traceable to the Bureau International des Poids et Mesures (BIPM), and the dissemination of S.I. quantities and units through the proper calibration of field instruments by the SSDLs. The Network has proved to be of value in improving national capabilities for instrument calibration and the awareness of better accuracy and traceability. Fifty-eight countries have nominated SSDLs for membership in the Network. Unfortunately, some of these SSDLs do not yet function as full members, perhaps because of some uncertainty as to their obligations concerning the Network. Consequently, the Scientific Committee which advises the Network Secretariat has recommended that a Charter be drawn up explaining the privileges, rights and duties of members in the Network which would strengthen their links to the international measurement system. In addition to the duties of members in the Network and the benefits that full members can receive, the Charter also describes how the Network functions and the scope of the work of the SSDLs. In producing this Charter, the advisory group has drawn heavily on the IAEA publication 'Secondary Standard Dosimetry Laboratories: Development and Trends' (1985) which summarizes the origin, development, status and prospects of the IAEA/WHO SSDL Network. The various appendices are effectively up-dates of different parts of this earlier publication, and the original drafting and reviewing bodies are given due recognition. The revisions take into account the experience the Agency has gained in coordinating the activities of the Network for more than 20 years

  5. The IAEA/WHO network of Secondary Standard Dosimetry Laboratories. SSDL network charter

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-04-01

    In 1976, the International Atomic Energy Agency (IAEA) together with the World Health Organization (WHO) established a Network of Secondary Standard Dosimetry Laboratories (SSDLs), known as the IAEA/WHO SSDL Network. This Network, through SSDLs designated by Member States, provides a direct linkage of national dosimetry standards to the international measurement system of standards traceable to the Bureau International des Poids et Mesures (BIPM), and the dissemination of S.I. quantities and units through the proper calibration of field instruments by the SSDLs. The Network has proved to be of value in improving national capabilities for instrument calibration and the awareness of better accuracy and traceability. Fifty-eight countries have nominated SSDLs for membership in the Network. Unfortunately, some of these SSDLs do not yet function as full members, perhaps because of some uncertainty as to their obligations concerning the Network. Consequently, the Scientific Committee which advises the Network Secretariat has recommended that a Charter be drawn up explaining the privileges, rights and duties of members in the Network which would strengthen their links to the international measurement system. In addition to the duties of members in the Network and the benefits that full members can receive, the Charter also describes how the Network functions and the scope of the work of the SSDLs. In producing this Charter, the advisory group has drawn heavily on the IAEA publication 'Secondary Standard Dosimetry Laboratories: Development and Trends' (1985) which summarizes the origin, development, status and prospects of the IAEA/WHO SSDL Network. The various appendices are effectively up-dates of different parts of this earlier publication, and the original drafting and reviewing bodies are given due recognition. The revisions take into account the experience the Agency has gained in coordinating the activities of the Network for more than 20 years.

  6. [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.

  7. Dosimetry using environmental and biological materials. Final report

    International Nuclear Information System (INIS)

    Haskell, E.; Kenner, G.; Hayes, R.

    1998-02-01

    This report summarizes a five year effort to improve the sensitivity and reliability of retrospective dosimetry methods, to collaborate with laboratories engaged in related research and to share the technology with startup laboratories seeking similar capabilities. This research program has focused on validation of electron paramagnetic resonance (EPR) as a dosimetry tool and on optimization of the technique by reducing the lower limits of detection, simplifying the process of sample preparation and analysis and speeding analysis to allow greater throughput in routine measurement situations. The authors have investigated the dosimetric signal of hard tissues in enamel, deorganified dentin, synthetic carbonated apatites and synthetic hydroxyapatite. This research has resulted in a total of 27 manuscripts which have been published, are in press, or have been submitted for publication. Of these manuscripts, 14 are included in this report and were indexed separately for inclusion in the data base

  8. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    Introduction. Over the past few years, network science has drawn attention from a large number of ... The qualitative properties of biological networks cannot ... Here, we study the underlying undirected structure of empirical biological networks.

  9. Design principles in biological networks

    Science.gov (United States)

    Goyal, Sidhartha

    Much of biology emerges from networks of interactions. Even in a single bacterium such as Escherichia coli, there are hundreds of coexisting gene and protein networks. Although biological networks are the outcome of evolution, various physical and biological constraints limit their functional capacity. The focus of this thesis is to understand how functional constraints such as optimal growth in mircoorganisms and information flow in signaling pathways shape the metabolic network of bacterium E. coli and the quorum sensing network of marine bacterium Vibrio harveyi, respectively. Metabolic networks convert basic elemental sources into complex building-blocks eventually leading to cell's growth. Therefore, typically, metabolic pathways are often coupled both by the use of a common substrate and by stoichiometric utilization of their products for cell growth. We showed that such a coupled network with product-feedback inhibition may exhibit limit-cycle oscillations which arise via a Hopf bifurcation. Furthermore, we analyzed several representative metabolic modules and find that, in all cases, simple product-feedback inhibition allows nearly optimal growth, in agreement with the predicted growth-rate by the flux-balance analysis (FBA). Bacteria have fascinating and diverse social lives. They display coordinated group behaviors regulated by quorum sensing (QS) systems. The QS circuit of V. harveyi integrates and funnels different ecological information through a common phosphorelay cascade to a set of small regulatory RNAs (sRNAs) that enables collective behavior. We analyzed the signaling properties and information flow in the QS circuit, which provides a model for information flow in signaling networks more generally. A comparative study of post-transcriptional and conventional transcriptional regulation suggest a niche for sRNAs in allowing cells to transition quickly yet reliably between distinct states. Furthermore, we develop a new framework for analyzing signal

  10. Dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Hurst, G S; Ritchie, R H; Sanders, F W; Reinhardt, P W; Auxier, J A; Wagner, E B; Callihan, A D; Morgan, K Z [Health Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN (United States)

    1962-03-15

    The methods of dosimetry used for investigation of the doses received by the individuals exposed in the Yugoslav accident were essentially those used in connection with the Oak Ridge Y-12 accident. An outline of the general scheme is as follows: When fast neutrons enter the human body, most of these are moderated to thermal energy and a small fraction of these are captured by a (n, gamma) process in Na sup 2 sup 3 , giving rise to Na sup 2 sup 4 , which by virtue of its emission of high-energy gamma rays with a half life of 14.8 h, is easily detected. It has been shown that the probability of capture, making Na sup 2 sup 4 , is not a strong function of the energy of the fast neutrons and that the probability of capture for neutrons is higher in the fast region than in the thermal region. Thus, the uniform distribution of Na sup 2 sup 3 in the human body provides an excellent means of normalizing the neutron exposure of an individual. in particular, for a given neutron energy spectrum the fast neutron dose is proportional to the ratio Na sup 2 sup 4 /Na sup 2 sup 3 in the body or in the blood system. This method of normalization is quite important in the dosimetry of radiation accidents since no assumptions need be made about the exact location of an individual at the time of the energy release. The importance of this fact can be made clear by reference to the Y-12 accident where it was shown by calculation of the neutron dose based on the known number of fissions and the stated location of the individual that one of the surviving individuals would have received a dose several times the lethal value. To accomplish the measurements described, the zero power R sub B reactor was operated in two ranges of power level, 'low' power and 'high 'power. Neutron leakage spectrum was obtained by multigroup approximation of the Boltzmann transport equation. Prompt gamma rays from fission products, from capture in the moderator and fuel cladding as well as in tank walls are given

  11. Dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Hurst, G S; Ritchie, R H; Sanders, F W; Reinhardt, P W; Auxier, J A; Wagner, E B; Callihan, A D; Morgan, K Z [Health Physics Division, Oak Ridge National Laboratory, Oak Ridge, TN (United States)

    1962-03-01

    The methods of dosimetry used for investigation of the doses received by the individuals exposed in the Yugoslav accident were essentially those used in connection with the Oak Ridge Y-12 accident. An outline of the general scheme is as follows: When fast neutrons enter the human body, most of these are moderated to thermal energy and a small fraction of these are captured by a (n, {gamma}) process in Na{sup 23}, giving rise to Na{sup 24}, which by virtue of its emission of high-energy gamma rays with a half life of 14.8 h, is easily detected. It has been shown that the probability of capture, making Na{sup 24}, is not a strong function of the energy of the fast neutrons and that the probability of capture for neutrons is higher in the fast region than in the thermal region. Thus, the uniform distribution of Na{sup 23} in the human body provides an excellent means of normalizing the neutron exposure of an individual. in particular, for a given neutron energy spectrum the fast neutron dose is proportional to the ratio Na{sup 24}/Na{sup 23} in the body or in the blood system. This method of normalization is quite important in the dosimetry of radiation accidents since no assumptions need be made about the exact location of an individual at the time of the energy release. The importance of this fact can be made clear by reference to the Y-12 accident where it was shown by calculation of the neutron dose based on the known number of fissions and the stated location of the individual that one of the surviving individuals would have received a dose several times the lethal value. To accomplish the measurements described, the zero power R{sub B} reactor was operated in two ranges of power level, 'low' power and 'high 'power. Neutron leakage spectrum was obtained by multigroup approximation of the Boltzman transport equation. Prompt gamma rays from fission products, from capture in the moderator and fuel cladding as well as in tank walls are given. A summary of the 4{pi

  12. Biological dosimetry studies for boron neutron capture therapy at the RA-1 research reactor facility

    International Nuclear Information System (INIS)

    Trivillin, Veronica A.; Heber, Elisa M.; Itoiz, Maria E.; Schwint, Amanda E.; Castillo, Jorge

    2004-01-01

    Initial physical dosimetry measurements have been completed using activation spectrometry and thermoluminescent dosimeters to characterize the BNCT facility developed at the RA-1 research reactor operated by the National Atomic Energy Commission in Buenos Aires. Biological dosimetry was performed employing the hamster cheek pouch oral cancer model previously validated for BNCT studies by our group. Results indicate that the RA-1 neutron source produces useful dose rates for BNCT studies but that some improvements in the initial configuration will be needed to optimize the spectrum for thermal-neutron BNCT research applications. (author)

  13. Biological and clinical dosimetry, July 1, 1964 to December 31, 1984. Final report

    International Nuclear Information System (INIS)

    Laughlin, J.S.; Zeitz, L.

    1986-01-01

    The goal was to develop systems for the determination of absorbed dose in biological research and clinical applications. The primary method under study is the local absorbed dose calorimeter. In addition, secondary dosimetric systems such as ionization chambers, chemical dosimeters and thermoluminescent dosimeters (TLD) are being developed and applied to provide an absolute basis for the evaluation and comparison of experiments, treatments and other procedures using radiation. In keeping with these objectives this project has accomplished significant advances in the following areas: (1) local absorbed dose calorimetry; (2) neutron dosimetry; (3) dosimetry of ultra-high intensity radiation sources; (4) solid state detector and germanium gamma camera program; (5) dosimetry for brachytherapy; and (6) ''non-isolated sensor'' calorimeters

  14. Biological dosimetry study in differentiated thyroid carcinoma patients treated with 131Iodine

    International Nuclear Information System (INIS)

    Vallerga, Maria Belen

    2008-11-01

    Biological Dosimetry allows individual dose assessments based on the effect produced by ionizing radiation on a given biological parameter. The current biological endpoint being scored is chromosomal aberrations, relying on a lymphocytes culture from the patient's blood. The measured yield of chromosome aberrations is referred to a calibration curve obtaining the whole body dose. Different scenarios of overexposure can be taken into account by modifying the calculations leading to the dose estimate. Differentiated Thyroid Carcinoma patients undergo thyroidectomy followed by internal radiotherapy with 131 I. The treatment's success entails the delivery of a lethal dose to the tumour within the maximum tolerable dose to a critical organ (blood doses over 2 Gy could lead to bone marrow depression). Currently, there is no established agreement for the selection of radioiodine dosage. Historically, the empiric approach, based on clinical and biochemical data, has been recommended. Nevertheless, this method may not be associated with optimal outcomes. On the other hand, the dosimetric approach attempts to determine the maximum allowable activity to be administered, establishing its biokinetics by a diagnostic 131 I study. The methodology may be modified to further individualized treatment, however it requires validation. Biological dosimetry provides an independent measure of radiotherapy effect, as such it might aid in the validation process. Nonetheless, biological dosimetry has traditionally been applied in cases of external and accidental overexposure to ionizing radiation. Accordingly, it is mandatory to assess its value in medical internal incorporations (main objective of the present study). The applied treatment strategy comprises whole body dose assessment by biological and internal dosimetry in order to administer a personalized therapeutic activity. Overall, 20 patients with differentiated thyroid carcinoma were included in the study. For biological dosimetry

  15. Biological transportation networks: Modeling and simulation

    KAUST Repository

    Albi, Giacomo; Artina, Marco; Foransier, Massimo; Markowich, Peter A.

    2015-01-01

    We present a model for biological network formation originally introduced by Cai and Hu [Adaptation and optimization of biological transport networks, Phys. Rev. Lett. 111 (2013) 138701]. The modeling of fluid transportation (e.g., leaf venation

  16. The use of the dicentric assay for biological dosimetry for radiation accidents in Bulgaria.

    Science.gov (United States)

    Hadjidekova, Valeria; Hristova, Rositsa; Ainsbury, Elizabeth A; Atanasova, Petya; Popova, Ljubomira; Staynova, Albena

    2010-02-01

    This paper details the construction of a 137Cs gamma calibration curve that has been established for dicentric assay and the testing and validation of the curve through biological dosimetry in three situations of suspected workplace overexposure that arose accidentally or through negligence or lack of appropriate safety measures. The three situations were: (1) suspected 137Cs contamination in a factory air supply; (2) suspected exposure to an industrial 192Ir source; and (3) accidental exposure of construction workers to radiation from a 60Co radiotherapy source in a hospital medical physics department. From a total of 24 potentially-exposed subjects, only one worker was found to have a statistically significant dose (0.16 Gy, 95% confidence intervals 0.02-0.43 Gy). In all other cases, the main function of the biological dosimetry was to reassure the subjects that any dose received was low.

  17. Radiation protection - Performance criteria for service laboratories performing biological dosimetry by cytogenetics

    International Nuclear Information System (INIS)

    2004-01-01

    This International Standard provides criteria for quality assurance and quality control, evaluation of the performance and the accreditation of biological dosimetry by cytogenetic service laboratories. This International Standard addresses: a) the confidentiality of personal information, for the customer and the service laboratory, b) the laboratory safety requirements, c) the calibration sources and calibration dose ranges useful for establishing the reference dose-effect curves allowing the dose estimation from chromosome aberration frequency, and the minimum detection levels, d) the scoring procedure for unstable chromosome aberrations used for biological dosimetry, e) the criteria for converting a measured aberration frequency into an estimate of absorbed dose, f) the reporting of results, g) the quality assurance and quality control, h) informative annexes containing examples of a questionnaire, instructions for customers, a data sheet for recording aberrations and a sample report

  18. Mammalian spermatogenesis as a new system for biologic dosimetry of ionizing irradiation

    International Nuclear Information System (INIS)

    Hacker, U.; Schumann, J.; Goehde, W.

    1982-01-01

    The radiation induced reduction of the number of DNA synthesizing cells (spermatogonia) is described using the fast-working flow cytophotometer. Since there is no shoulder in the initial part of the dose response curve this model of biologic dosimetry is very sensitive. The D 50 value is 0.25 Gy; a radiation exposure of only 0.1 Gy can be detected. (Auth.)

  19. Mammalian spermatogenesis as a new system for biologic dosimetry of ionizing irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Hacker, U; Schumann, J; Goehde, W [Muenster Univ. (Germany, F.R.). Radiologische Klinik

    1982-01-01

    The radiation induced reduction of the number of DNA synthesizing cells (spermatogonia) is described using the fast-working flow cytophotometer. Since there is no shoulder in the initial part of the dose response curve this model of biologic dosimetry is very sensitive. The D/sub 50/ value is 0.25 Gy; a radiation exposure of only 0.1 Gy can be detected.

  20. Towards Establishing Capacity for Biological Dosimetry at Ghana Atomic Energy Commission.

    Science.gov (United States)

    Achel, Daniel Gyingiri; Achoribo, Elom; Agbenyegah, Sandra; Adaboro, Rudolph M; Donkor, Shadrack; Adu-Bobi, Nana A K; Agyekum, Akwasi A; Akuamoa, Felicia; Tagoe, Samuel N; Kyei, Kofi A; Yarney, Joel; Serafin, Antonio; Akudugu, John M

    2016-01-01

    The aim of this study was not only to obtain basic technical prerequisites for the establishment of capacity of biological dosimetry at the Ghana Atomic Energy Commission (GAEC) but also to stimulate interest in biological dosimetry research in Ghana and Sub-Saharan Africa. Peripheral blood from four healthy donors was exposed to different doses (0-6 Gy) of gamma rays from a radiotherapy machine and lymphocytes were subsequently stimulated, cultured, and processed according to standard protocols for 48-50 h. Processed cells were analyzed for the frequencies of dicentric and centric ring chromosomes. Radiation dose delivered to the experimental model was verified using GafChromic® EBT films in parallel experiments. Basic technical prerequisites for the establishment of capacity of biological dosimetry in the GAEC have been realized and expertise in the dicentric chromosome assay consolidated. We successfully obtained preliminary cytogenetic data for a dose-response relationship of the irradiated blood lymphocytes. The data strongly indicate the existence of significant linear (α) and quadratic (β) components and are consistent with those published for the production of chromosome aberrations in comparable absorbed dose ranges.

  1. 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 ...

  2. Radiation protection dosimetry in medicine - Report of the working group n.9 of the European radiation dosimetry group (EURADOS) - coordinated network for radiation dosimetry (CONRAD - contract EC N) fp6-12684; Dosimetrie pour la radioprotection en milieu medical - rapport du groupe de travail n. 9 du European radiation dosimetry group (EURADOS) - coordinated netword for radiation dosimetry (CONRAD - contrat CE fp6-12684)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2009-07-01

    This report present the results achieved within the frame of the work the WP 7 (Radiation Protection Dosimetry of Medical Staff) of the coordination action CONRAD (Coordinated Network for Radiation Dosimetry) funded through the 6. EU Framework Program. This action was coordinated by EURADOS (European Radiation Dosimetry Group). EURADOS is an organization founded in 1981 to advance the scientific understanding and the technical development of the dosimetry of ionising radiation in the fields of radiation protection, radiobiology, radiation therapy and medical diagnosis by promoting collaboration between European laboratories. WP7 coordinates and promotes European research for the assessment of occupational exposures to staff in therapeutic and diagnostic radiology workplaces. Research is coordinated through sub-groups covering three specific areas: 1. Extremity dosimetry in nuclear medicine and interventional radiology: this sub-group coordinates investigations in the specific fields of the hospitals and studies of doses to different parts of the hands, arms, legs and feet; 2. Practice of double dosimetry: this sub-group reviews and evaluates the different methods and algorithms for the use of dosemeters placed above and below lead aprons in large exposure during interventional radiology procedures, especially to determine effective doses to cardiologists during cardiac catheterization; and 3. Use of electronic personal dosemeters in interventional radiology: this sub-group coordinates investigations in laboratories and hospitals, and intercomparisons with passive dosemeters with the aim to enable the formulation of standards. (authors)

  3. General guidelines for safe and expeditious international transport of samples subjected to biological dosimetry assessment.

    Science.gov (United States)

    Di Giorgio, Marina; Radl, Analía; Taja, María R; Bubniak, Ruth; Deminge, Mayra; Sapienza, Carla; Vázquez, Marina; Baciu, Florian; Kenny, Pat

    2014-06-01

    It has been observed that victims of accidental overexposures show better chance of survival if they receive medical treatment early. The increased risk of scenarios involving mass casualties has stimulated the scientific community to develop tools that would help the medical doctors to treat victims. The biological dosimetry has become a routine test to estimate the dose, supplementing physical and clinical dosimetry. In case of radiation emergencies, in order to provide timely and effectively biological dosimetry assistance it is essential to guarantee an adequate transport of blood samples in principal, for providing support to countries that do not have biodosimetry laboratories. The objective of the present paper is to provide general guidelines, summarised in 10 points, for timely and proper receiving and sending of blood samples under National and International regulations, for safe and expeditious international transport. These guidelines cover the classification, packaging, marking, labelling, refrigeration and documentation requirements for the international shipping of blood samples and pellets, to provide assistance missions with a tool that would contribute with the preparedness for an effective biodosimetric response in cases of radiological or nuclear emergencies. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. Role of accelerator mass spectrometry in biological dosimetry

    International Nuclear Information System (INIS)

    Felton, J.S.; Turteltaub, K.W.; Frantz, C.; Vogel, J.S.; Gledhill, B.L.

    1992-01-01

    Understanding risks from exposures to carcinogens and other chemicals depends upon measurement of their dose to target tissues and their reactivity with critical macromolecules. The authors have used AMS detection of radio-isotopes to assess doses and reactivities at low, environmentally relevant doses. Several biomedical investigations show the effectiveness of quantification of biologically important events at extremely high sensitivity with AMS. Specifically, they have measured the addition of environmental carcinogens such as 2-amino-3,8-dimethylimidazo[4,5-f]-quinoaxaline (MelQx), a chemical found in cooked food, to DNA at concentrations relevant to human exposure. Other low level detection problems in biology, such as immunoassay assessment of small environmental chemicals, is being developed with attomole sensitivity. AMS also aids the assessment of genotoxic risks from chemicals by quantifying the binding of labeled chemicals to DNA. The very toxic and potent carcinogen, tetrachlorodibenzo-p-dioxin (TCDD) was assessed for DNA binding, but no detectable radiocarbon-labeled TCDD was found associated with mouse liver DNA at less than systematically toxic levels. The data indicate that a mutation mechanism does not mediate TCDD carcinogenesis

  5. Development of radiological emergency preparedness and biological dosimetry technology

    Energy Technology Data Exchange (ETDEWEB)

    Han, Moon Hee; Kim, In Gyoo; Kim, Kook Chan; Kim, Eun Han; Suh, Kyung Suk; Hwang, Won Tae; Choi, Young Gil; Shim, Hae Won; Lee, Jeong Ho; Lee, Kang Suk

    1999-04-01

    Large-scale field tracer experiments have been conducted on Ulchin and Wolsung nuclear sites for the purpose of validating FADAS and of analyzing the environmental characteristics around the nuclear site. The most influential factor in atmospheric dispersion is the meteorological condition. During the experiment, meteorological data were measured on the release point and the selected positions among sampling points. Once radioactive materials are released to the atmosphere, members of public may be exposed through the environmental media such as air, soil and foods. Therefore, to protect the public, adequate countermeasures should be taken at due time for those exposure pathways. Both processes of justification and optimization are applied to a countermeasure simultaneously for decision-making. The work scope of biological research for the radiation protection had contained the search of biological microanalytic methods for the assessment of health effect by radiation and toxic agents, the standardization of human t-lymphocyte cell culture and polymerase chain reaction, T-cell clonal assay, and the quantification of mutation frequency in hypoxanthine (guanine) phosphoribosyl transferase (hprt) gene locus by single exposure or combined exposure. Especially, the polymerase chain reaction methods by usage of reverse transcriptase had been developed to analyze of gene product by {gamma} - radiation and chemical (pentachlorophenol) agent exposure, and investigate the point mutation in hprt gene locus of T-lymphocytes. (author)

  6. Development of radiological emergency preparedness and biological dosimetry technology

    International Nuclear Information System (INIS)

    Han, Moon Hee; Kim, In Gyoo; Kim, Kook Chan; Kim, Eun Han; Suh, Kyung Suk; Hwang, Won Tae; Choi, Young Gil; Shim, Hae Won; Lee, Jeong Ho; Lee, Kang Suk

    1999-04-01

    Large-scale field tracer experiments have been conducted on Ulchin and Wolsung nuclear sites for the purpose of validating FADAS and of analyzing the environmental characteristics around the nuclear site. The most influential factor in atmospheric dispersion is the meteorological condition. During the experiment, meteorological data were measured on the release point and the selected positions among sampling points. Once radioactive materials are released to the atmosphere, members of public may be exposed through the environmental media such as air, soil and foods. Therefore, to protect the public, adequate countermeasures should be taken at due time for those exposure pathways. Both processes of justification and optimization are applied to a countermeasure simultaneously for decision-making. The work scope of biological research for the radiation protection had contained the search of biological microanalytic methods for the assessment of health effect by radiation and toxic agents, the standardization of human t-lymphocyte cell culture and polymerase chain reaction, T-cell clonal assay, and the quantification of mutation frequency in hypoxanthine (guanine) phosphoribosyl transferase (hprt) gene locus by single exposure or combined exposure. Especially, the polymerase chain reaction methods by usage of reverse transcriptase had been developed to analyze of gene product by γ - radiation and chemical (pentachlorophenol) agent exposure, and investigate the point mutation in hprt gene locus of T-lymphocytes. (author)

  7. Development of radiation biological dosimetry and treatment of radiation-induced damaged tissue

    International Nuclear Information System (INIS)

    Cho, Chul Koo; Kim, Tae Hwan; Lee, Yun Sil

    2000-04-01

    Util now, only a few methods have been developed for radiation biological dosimetry such as conventional chromosome aberration and micronucleus in peripheral blood cell. However, because these methods not only can be estimated by the expert, but also have a little limitation due to need high technique and many times in the case of radiation accident, it is very difficult to evaluate the absorbed dose of victims. Therefore, we should develop effective, easy, simple and rapid biodosimetry and its guideline(triage) to be able to be treated the victims as fast as possible. We established the apoptotic fragment assay, PCC, comet assay, and micronucleus assay which was the significant relationship between dose and cell damages to evaluate the irradiated dose as correct and rapid as possible using lymphocytes and crypt cells, and compared with chromosome dosimetry and micronucleus assay

  8. Development of radiation biological dosimetry and treatment of radiation-induced damaged tissue

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Chul Koo; Kim, Tae Hwan; Lee, Yun Sil [and others

    2000-04-01

    Util now, only a few methods have been developed for radiation biological dosimetry such as conventional chromosome aberration and micronucleus in peripheral blood cell. However, because these methods not only can be estimated by the expert, but also have a little limitation due to need high technique and many times in the case of radiation accident, it is very difficult to evaluate the absorbed dose of victims. Therefore, we should develop effective, easy, simple and rapid biodosimetry and its guideline(triage) to be able to be treated the victims as fast as possible. We established the apoptotic fragment assay, PCC, comet assay, and micronucleus assay which was the significant relationship between dose and cell damages to evaluate the irradiated dose as correct and rapid as possible using lymphocytes and crypt cells, and compared with chromosome dosimetry and micronucleus assay.

  9. Biological dosimetry, scopes and limitations; Dosimetria biologica, alcances y limitaciones

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero C, C.; Brena V, M. [Departamento de Biologia, Instituto Nacional de Investigaciones Nucleares, C.P. 52045 Salazar, Estado de Mexico (Mexico)

    1999-07-01

    The analysis of the aberrations in chromosomes is an alternative to establish the exposure dose to the radiation, when the information provided by the traditional physical methods is insufficient. There are diverse causes by which it can reached to apply an alternative system, such is the case of exposures of another persons to the management of radiation sources, which not carry physical dosemeter. Contrary case is to the occupational exposure personnel (OEP), what must to utilize some system for determining the exposure dose, even so can be needed the case for more information. In any case, the cells from the affected person are the alternative without the biological system be overlap to the physical, it is complementary. (Author)

  10. Biological transportation networks: Modeling and simulation

    KAUST Repository

    Albi, Giacomo

    2015-09-15

    We present a model for biological network formation originally introduced by Cai and Hu [Adaptation and optimization of biological transport networks, Phys. Rev. Lett. 111 (2013) 138701]. The modeling of fluid transportation (e.g., leaf venation and angiogenesis) and ion transportation networks (e.g., neural networks) is explained in detail and basic analytical features like the gradient flow structure of the fluid transportation network model and the impact of the model parameters on the geometry and topology of network formation are analyzed. We also present a numerical finite-element based discretization scheme and discuss sample cases of network formation simulations.

  11. Attentional Networks and Biological Motion

    Directory of Open Access Journals (Sweden)

    Chandramouli Chandrasekaran

    2010-03-01

    Full Text Available Our ability to see meaningful actions when presented with pointlight traces of human movement is commonly referred to as the perception of biological motion. While traditionalexplanations have emphasized the spontaneous and automatic nature of this ability, morerecent findings suggest that attention may play a larger role than is typically assumed. Intwo studies we show that the speed and accuracy of responding to point-light stimuli is highly correlated with the ability to control selective attention. In our first experiment we measured thresholds for determining the walking direction of a masked point-light figure, and performance on a range of attention-related tasks in the same set of observers. Mask-density thresholds for the direction discrimination task varied quite considerably from observer to observer and this variation was highly correlated with performance on both Stroop and flanker interference tasks. Other components of attention, such as orienting, alerting and visual search efficiency, showed no such relationship. In a second experiment, we examined the relationship between the ability to determine the orientation of unmasked point-light actions and Stroop interference, again finding a strong correlation. Our results are consistent with previous research suggesting that biological motion processing may requite attention, and specifically implicate networks of attention related to executive control and selection.

  12. Biological dosimetry following exposure to neutrons in a criticality accident

    Energy Technology Data Exchange (ETDEWEB)

    Lindholm, C. (Radiation and Nuclear Safety Authority, STUK (Finland)); Wojcik, A. (Stockholm Univ. (SU), Stockholm (Sweden)); Jaworska, A. (Norwegian Radiation Protection Authority (NRPA) (Norway))

    2011-01-15

    The aim of the BIONCA project was to implement cytogenetic techniques for biodosimetry purposes in the Nordic countries. The previous NKS-funded biodosimetry activities (BIODOS and BIOPEX) concentrated on experiments using gamma-irradiation and on developing the PCC ring assay for biodosimetry. Experiments conducted during the present BIONCA project has broadened the biodosimetry capacity of the Nordic countries to include dose estimation of exposure to neutrons for both PCC ring and dicentric chromosome techniques. In 2009, experiments were conducted for establishing both PCC ring and dicentric dose calibration curves. Neutron irradiation of human whole blood obtained from two volunteers was conducted in the Netherlands at the Petten reactor. Cell cultures and analysis of whole blood exposed to eight doses between 0 and 10 Gy were performed for both techniques. For the dicentric assay, excellent uniformity in dose calibration for data from both SU and STUK was observed. For PCC rings, the SU and STUK curves were not equally congruent, probably due to the less uniform scoring criteria. However, both curves displayed strong linearity throughout the dose range. In 2010, an exercise was conducted to simulate a criticality accident and to test the validity of the established dose calibration curves. For accident simulation, 16 blood samples were irradiated in Norway at the Kjeller reactor and analysed for dose estimation with both assays. The results showed that, despite a different com-position of the radiation beams in Petten and Kjeller, good dose estimates were obtained. The activity has provided good experience on collaboration required in radiation emergency situations where the biodosimetry capacity and resources of one laboratory may be inadequate. In this respect, the project has strengthened the informal network between the Nordic countries: STUK, the Finnish Radiation and Nuclear Safety Authority, NRPA, the Norwegian Radiation Protection Authority and SU

  13. Biological dosimetry intercomparison exercise: an evaluation of Triage and routine mode results by robust methods

    International Nuclear Information System (INIS)

    Di Giorgio, M.; Vallerga, M.B.; Radl, A.; Taja, M.R.; Barquinero, J.F.; Seoane, A.; De Luca, J.; Guerrero Carvajal, Y.C.; Stuck Oliveira, M.S.; Valdivia, P.; García Lima, O.; Lamadrid, A.; González Mesa, J.; Romero Aguilera, I.; Mandina Cardoso, T.; Arceo Maldonado, C.; Espinoza, M.E.; Martínez López, W.; Lloyd, D.C.; Méndez Acuña, L.; Di Tomaso, M.V.; Roy, L.; Lindholm, C.; Romm, H.; Güçlü, I.

    2011-01-01

    Well-defined protocols and quality management standards are indispensable for biological dosimetry laboratories. Participation in periodic proficiency testing by interlaboratory comparisons is also required. This harmonization is essential if a cooperative network is used to respond to a mass casualty event. Here we present an international intercomparison based on dicentric chromosome analysis for dose assessment performed in the framework of the IAEA Regional Latin American RLA/9/054 Project. The exercise involved 14 laboratories, 8 from Latin America and 6 from Europe. The performance of each laboratory and the reproducibility of the exercise were evaluated using robust methods described in ISO standards. The study was based on the analysis of slides from samples irradiated with 0.75 (DI) and 2.5 Gy (DII). Laboratories were required to score the frequency of dicentrics and convert them to estimated doses, using their own dose-effect curves, after the analysis of 50 or 100 cells (triage mode) and after conventional scoring of 500 cells or 100 dicentrics. In the conventional scoring, at both doses, all reported frequencies were considered as satisfactory, and two reported doses were considered as questionable. The analysis of the data dispersion among the dicentric frequencies and among doses indicated a better reproducibility for estimated doses (15.6% for DI and 8.8% for DII) than for frequencies (24.4% for DI and 11.4% for DII), expressed by the coefficient of variation. In the two triage modes, although robust analysis classified some reported frequencies or doses as unsatisfactory or questionable, all estimated doses were in agreement with the accepted error of ±0.5 Gy. However, at the DI dose and for 50 scored cells, 5 out of the 14 reported confidence intervals that included zero dose and could be interpreted as false negatives. This improved with 100 cells, where only one confidence interval included zero dose. At the DII dose, all estimations fell within

  14. Transient impedance changes in venous endothelial monolayers as a biological radiation dosimetry response

    Directory of Open Access Journals (Sweden)

    Erik Fossum Young

    2012-10-01

    Full Text Available In March of 2011, a magnitude 9.0 earthquake and subsequent 14 m-high tsunami caused major damage to the Fukushima Daiichi nuclear power plant in Japan.  While cancer incidence in the radiation-exposed population is a logical concern, the complex effects of radiation on the heart and cardiovascular system are also of interest.  Immediate and early vascular radiation effects could be exploited as a dosimetry modality.  To test whether non-coronary vasculature exhibited transient perturbation in barrier function, video microscopy studies and Electric Cell Substrate Impedance Sensing technology were used to probe very subtle changes in primary human vascular endothelium.  Human umbilical vein endothelial cell (HUVEC monolayers exhibit a transient, statistically significant decrease (P = 0.017 in monolayer resistance 3 h after irradiation with 5.0 Gy of g rays.  Radiation induced perturbations in HUVEC monolayer permeability are similar in magnitude and kinetics to those observed in coronary arterial endothelium.  Therefore, at least two types of vasculature respond to radiation on ECIS arrays with an early transient disruption in permeability.  The finding supports the use of early passage HUVECs for use in bioelectric dosimetry studies of vasculature and suggests that permeability of vessels could potentially serve as a biological dosimetry tool.

  15. Conventional radiation-biological dosimetry using frequencies of unstable chromosome aberrations

    International Nuclear Information System (INIS)

    Ramalho, Adriana T.; Costa, Maria Lucia P.; Oliveira, Monica S.

    1998-01-01

    Frequency of chromosome aberrations detected by conventional cytogenetics is a very useful parameter in biological radiodosimetry. It can be used for estimating absorbed doses in individuals working with radioactive sources and individuals accidentally exposed to radiation. In the first case subjects wear physical dosimeters as a routine safety habit. The laboratory at the Institute of Radioprotection and Dosimetry (IRD, Brazil) has been using conventional cytogenetic analysis to complement data obtained by physical dosimetry since 1983. Until now, more than one hundred cases were investigated where individual physical dosimeters detected occupational exposure (above the safety limits allowed). In total, only 34% of these cases were confirmed by conventional cytogenetic dosimetry. Also, conventional cytogenetic analysis following the radiation accident of Goiania (Brazil) in 1987 have been used. Peripheral lymphocytes from 129 exposed or potentially exposed individuals were analyzed for the frequencies of unstable chromosomal aberrations (dicentrics, centric rings and acentrics fragments) to estimate absorbed radiation doses. During the emergency period, doses were estimated to help immediate medical treatment using in vitro calibration curves produced before the accident. Later on, doses were assessed once more using new in vitro calibration curves. A drawback of this technique is that unstable aberrations are lost after exposure. To investigate the mean lifespan of lymphocytes containing dicentric and ring aberrations, we have followed 15 victims of the Goiania accident over all these years. Results suggest that the disappearance of unstable aberrations is dose-dependent. This could explain the variation in the results found among studies in this field

  16. Conventional radiation-biological dosimetry using frequencies of unstable chromosome aberrations

    Energy Technology Data Exchange (ETDEWEB)

    Ramalho, Adriana T.; Costa, Maria Lucia P.; Oliveira, Monica S. [Institute of Radioprotection and Dosimetry (IRD), National Commission of Nuclear Energy (CNEN), Av. Salvador Allende, Cx. P. 37750, Rio de Janeiro 22.780-160 (Brazil)

    1998-08-03

    Frequency of chromosome aberrations detected by conventional cytogenetics is a very useful parameter in biological radiodosimetry. It can be used for estimating absorbed doses in individuals working with radioactive sources and individuals accidentally exposed to radiation. In the first case subjects wear physical dosimeters as a routine safety habit. The laboratory at the Institute of Radioprotection and Dosimetry (IRD, Brazil) has been using conventional cytogenetic analysis to complement data obtained by physical dosimetry since 1983. Until now, more than one hundred cases were investigated where individual physical dosimeters detected occupational exposure (above the safety limits allowed). In total, only 34% of these cases were confirmed by conventional cytogenetic dosimetry. Also, conventional cytogenetic analysis following the radiation accident of Goiania (Brazil) in 1987 have been used. Peripheral lymphocytes from 129 exposed or potentially exposed individuals were analyzed for the frequencies of unstable chromosomal aberrations (dicentrics, centric rings and acentrics fragments) to estimate absorbed radiation doses. During the emergency period, doses were estimated to help immediate medical treatment using in vitro calibration curves produced before the accident. Later on, doses were assessed once more using new in vitro calibration curves. A drawback of this technique is that unstable aberrations are lost after exposure. To investigate the mean lifespan of lymphocytes containing dicentric and ring aberrations, we have followed 15 victims of the Goiania accident over all these years. Results suggest that the disappearance of unstable aberrations is dose-dependent. This could explain the variation in the results found among studies in this field

  17. Measuring the evolutionary rewiring of biological networks.

    Directory of Open Access Journals (Sweden)

    Chong Shou

    Full Text Available We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of "commonplace" networks such as family trees, co-authorships and linux-kernel function dependencies.

  18. Development of technology for biological dosimetry -A study on the radiation and environmental safety-

    International Nuclear Information System (INIS)

    Lee, Kang Suk; Cheon, Ki Jeong; Kim, Kook Chan; Kim, Jin Kyu; Kim, Sang Bok; Kim, In Kyu; Park, Hyo Kook

    1994-07-01

    α-amylase showed a significant increase in its activity when exposed to radiation of 0.1 Gy. However it had no relationship with radiation dose. Enzyme activities in liver tissue showed similar changes to those in serum. Among others, changes in acid phosphatase activity were highly related to radiation dose. Of acute phase proteins in serum, CRP, ceruloplasmin and haptoglobin positively responded to radiation while albumin did negatively. ELISA proved to be an efficient method to detect changes in serum protein level. Finally the measurements of changes in APRs using ELISA could provide an useful tools for biological dosimetry. (Author)

  19. Studies with encapsulated 125I sources: dosimetry for determination of relative biological effectiveness

    International Nuclear Information System (INIS)

    Goldhagen, P.; Freeman, M.L.; Hall, E.J.

    1981-01-01

    During the past year, members of this laboratory have measured the Relative Biological Effectiveness (RBE) of photons from encapsulated 125 I sources (mean energy = 28.33 keV) using 661.6 keV 137 Cs gamma rays as a standard for comparison. These experiments were performed at clinically relevant dose rates and used reduction of the reproductive viability of mammalian cells as an endpoint. This section will discuss how dosimetry problems special to 125 I influence the design of the apparatus and will describe the ionization chamber to be used for measuring dose rates from both 125 I and 137 Cs photons

  20. Chromosomal analysis and application of biological dosimetry in two cases of apparent over exposure

    International Nuclear Information System (INIS)

    Guerrero C, C.; Brena V, M.

    2002-01-01

    The gamma radiation calibration curve of 60 Co is used which was generated in the ININ Laboratory of Biology to calculate the exposure dose of two workers whose dosemeters marked values above of the limit allowed. The analysis indicates that in a first case, the aberrations frequency corresponded to the basal value, therefore there is not over exposure. The aberrations frequency of the second case is lightly above to the basal value and therefore the probability favors to what the physical dosimetry indicates. (Author)

  1. Bibliographical database of radiation biological dosimetry and risk assessment: Part 1, through June 1988

    Energy Technology Data Exchange (ETDEWEB)

    Straume, T.; Ricker, Y.; Thut, M.

    1988-08-29

    This database was constructed to support research in radiation biological dosimetry and risk assessment. Relevant publications were identified through detailed searches of national and international electronic databases and through our personal knowledge of the subject. Publications were numbered and key worded, and referenced in an electronic data-retrieval system that permits quick access through computerized searches on publication number, authors, key words, title, year, and journal name. Photocopies of all publications contained in the database are maintained in a file that is numerically arranged by citation number. This report of the database is provided as a useful reference and overview. It should be emphasized that the database will grow as new citations are added to it. With that in mind, we arranged this report in order of ascending citation number so that follow-up reports will simply extend this document. The database cite 1212 publications. Publications are from 119 different scientific journals, 27 of these journals are cited at least 5 times. It also contains reference to 42 books and published symposia, and 129 reports. Information relevant to radiation biological dosimetry and risk assessment is widely distributed among the scientific literature, although a few journals clearly dominate. The four journals publishing the largest number of relevant papers are Health Physics, Mutation Research, Radiation Research, and International Journal of Radiation Biology. Publications in Health Physics make up almost 10% of the current database.

  2. Bibliographical database of radiation biological dosimetry and risk assessment: Part 1, through June 1988

    International Nuclear Information System (INIS)

    Straume, T.; Ricker, Y.; Thut, M.

    1988-01-01

    This database was constructed to support research in radiation biological dosimetry and risk assessment. Relevant publications were identified through detailed searches of national and international electronic databases and through our personal knowledge of the subject. Publications were numbered and key worded, and referenced in an electronic data-retrieval system that permits quick access through computerized searches on publication number, authors, key words, title, year, and journal name. Photocopies of all publications contained in the database are maintained in a file that is numerically arranged by citation number. This report of the database is provided as a useful reference and overview. It should be emphasized that the database will grow as new citations are added to it. With that in mind, we arranged this report in order of ascending citation number so that follow-up reports will simply extend this document. The database cite 1212 publications. Publications are from 119 different scientific journals, 27 of these journals are cited at least 5 times. It also contains reference to 42 books and published symposia, and 129 reports. Information relevant to radiation biological dosimetry and risk assessment is widely distributed among the scientific literature, although a few journals clearly dominate. The four journals publishing the largest number of relevant papers are Health Physics, Mutation Research, Radiation Research, and International Journal of Radiation Biology. Publications in Health Physics make up almost 10% of the current database

  3. Comparing biological networks via graph compression

    Directory of Open Access Journals (Sweden)

    Hayashida Morihiro

    2010-09-01

    Full Text Available Abstract Background Comparison of various kinds of biological data is one of the main problems in bioinformatics and systems biology. Data compression methods have been applied to comparison of large sequence data and protein structure data. Since it is still difficult to compare global structures of large biological networks, it is reasonable to try to apply data compression methods to comparison of biological networks. In existing compression methods, the uniqueness of compression results is not guaranteed because there is some ambiguity in selection of overlapping edges. Results This paper proposes novel efficient methods, CompressEdge and CompressVertices, for comparing large biological networks. In the proposed methods, an original network structure is compressed by iteratively contracting identical edges and sets of connected edges. Then, the similarity of two networks is measured by a compression ratio of the concatenated networks. The proposed methods are applied to comparison of metabolic networks of several organisms, H. sapiens, M. musculus, A. thaliana, D. melanogaster, C. elegans, E. coli, S. cerevisiae, and B. subtilis, and are compared with an existing method. These results suggest that our methods can efficiently measure the similarities between metabolic networks. Conclusions Our proposed algorithms, which compress node-labeled networks, are useful for measuring the similarity of large biological networks.

  4. Network Reconstruction of Dynamic Biological Systems

    OpenAIRE

    Asadi, Behrang

    2013-01-01

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

  5. Effect of contrast agent administration on consequences of dosimetry and biology in radiotherapy planning

    International Nuclear Information System (INIS)

    Lo, Ching-Jung; Yang, Pei-Ying; Chao, Tsi-Chian; Tu, Shu-Ju

    2015-01-01

    In the treatment planning of radiation therapy, patients may be administrated with contrast media in CT scanning to assist physicians for accurate delineation of the target or organs. However, contrast media are not used in patients during the treatment delivery. In particular, contrast media contain materials with high atomic numbers and dosimetric variations may occur between scenarios where contrast media are present in treatment planning and absent in treatment delivery. In this study we evaluate the effect of contrast media on the dosimetry and biological consequence. An analytical phantom based on AAPM TG 119 and five sets of CT images from clinical patients are included. Different techniques of treatment planning are considered, including 1-field AP, 2-field AP+PA, 4-field box, 7-field IMRT, and RapidArc. RapidArc is a recent technique of volumetric modulated arc therapy and is used in our study of contrast media in clinical scenarios. The effect of RapidArc on dosimetry and biological consequence for administration of contrast media in radiotherapy is not discussed previously in literature. It is shown that dose difference is reduced as the number of external beams is increased, suggesting RapidArc may be favored to be used in the treatment planning enhanced by contrast media. Linear trend lines are fitted for assessment of percent dose differences in the planning target volume versus concentrations of contrast media between plans where contrast media are present and absent, respectively

  6. Calibration curves for biological dosimetry by drug-induced prematurely condensed chromosomes in human lymphocytes

    International Nuclear Information System (INIS)

    Kang, C. M.; Chung, H. C.; Cho, C. K.

    2002-01-01

    To develop the cytogenetic tool to detect chromosome damages after high dose exposure with 60 Coγ- rays, dose-response curves were measured for induction of prematurely condensed chromosomes (PCC) in peripheral lymphocytes. Blood was obtained from 10 different healthy donors, and given okadaic acid (OA) 500nM in cultured lymphocytes 1h after radiation exposure. Cells were analyzed by the frequencies of OA-induced PCC rings because it is difficult to obtain mitotic chromosomes using a conventional chromosome aberration (CA). PCC-rings were scored in cells exposed in the dose range of 0.2-16Gy. The frequency of the cells with PCC and the dose-response relationship for the yield of PCC rings were examined in the irradiated lymphocytes. The yield of PCC-rings increased with dose dependent-manner up to 16Gy. The observed dose-effect relationship for the percentage of cells with PCC-rings was calculated by linear-quadratic model. This technique can be applied to biological dosimetry of radiation exposures involving whole body irradiation to allow damaged chromosomes to be detected with great sensitivity. Detection of okadaic acid-induced PCC rings is a useful method up to 16Gy or more doses in estimating the absorbed doses of victims after high dose exposure. Calibration curves described in this paper will be used in our laboratory for biological dosimetry by PCC-ring after a high dose exposure

  7. Biological dosimetry in case of combined radiation injuries. Biologicheskaya dozimetriya pri kombinirovannykh radiatsionnykh porazheniyakh

    Energy Technology Data Exchange (ETDEWEB)

    Vladimirov, V G; Teslenko, V M

    1990-11-01

    The state of biological dosimetry methods and prospects for their development are considered. Attention is paid to biological indicators of radiation injuries caused by nuclear weapons. It is noted, that determination of the number of lymphocytes in the blood in case of combined radiation injuries should be concerned with great care and in each case the analysis results should reffered to critically and supported by the data from other investigations. Promissing are the methods related to dermination of reticulocyte number in the peripheral blood within the irradiation dose range, causing bone marrow form of radiation syndrome, method of leukocyte adhesion and some other methods based on the change of biophysical caracteristics of cell membranes. To increase the information efficiency it is necessary to combine these methods with the methods, based on genetic change registration, and to develop a combined method.

  8. Accreditation and training on internal dosimetry in a laboratory network in Brazil: an increasing demand.

    Science.gov (United States)

    Dantas, B M; Dantas, A L A; Acar, M E D; Cardoso, J C S; Julião, L M Q C; Lima, M F; Taddei, M H T; Arine, D R; Alonso, T; Ramos, M A P; Fajgelj, A

    2011-03-01

    In recent years, Brazilian Nuclear Programme has been reviewed and updated by government authorities in face of the demand for energy supply and its associated environmental constraints. The immediate impact of new national programmes and projects in nuclear field is the increase in the number of exposed personnel and the consequent need for reliable dosimetry services in the country. Several Technical Documents related to internal dosimetry have been released by the International Atomic Energy Agency and International Commission on Radiological Protection. However, standard bioassay procedures and methodologies for bioassay data interpretation are still under discussion and, in some cases, both in routine and emergency internal monitoring, procedures can vary from one laboratory to another and responses may differ markedly among Dosimetry Laboratories. Thus, it may be difficult to interpret and use bioassay data generated from different laboratories of a network. The main goal of this work is to implement a National Network of Laboratories aimed to provide reliable internal monitoring services in Brazil. The establishment of harmonised in vivo and in vitro radioanalytical techniques, dose assessment methods and the implementation of the ISO/IEC 17025 requirements will result in the recognition of technical competence of the network.

  9. Radiation protection dosimetry in medicine - Report of the working group n.9 of the European radiation dosimetry group (EURADOS) - coordinated network for radiation dosimetry (CONRAD - contract EC N) fp6-12684

    International Nuclear Information System (INIS)

    2009-01-01

    This report present the results achieved within the frame of the work the WP 7 (Radiation Protection Dosimetry of Medical Staff) of the coordination action CONRAD (Coordinated Network for Radiation Dosimetry) funded through the 6. EU Framework Program. This action was coordinated by EURADOS (European Radiation Dosimetry Group). EURADOS is an organization founded in 1981 to advance the scientific understanding and the technical development of the dosimetry of ionising radiation in the fields of radiation protection, radiobiology, radiation therapy and medical diagnosis by promoting collaboration between European laboratories. WP7 coordinates and promotes European research for the assessment of occupational exposures to staff in therapeutic and diagnostic radiology workplaces. Research is coordinated through sub-groups covering three specific areas: 1. Extremity dosimetry in nuclear medicine and interventional radiology: this sub-group coordinates investigations in the specific fields of the hospitals and studies of doses to different parts of the hands, arms, legs and feet; 2. Practice of double dosimetry: this sub-group reviews and evaluates the different methods and algorithms for the use of dosemeters placed above and below lead aprons in large exposure during interventional radiology procedures, especially to determine effective doses to cardiologists during cardiac catheterization; and 3. Use of electronic personal dosemeters in interventional radiology: this sub-group coordinates investigations in laboratories and hospitals, and intercomparisons with passive dosemeters with the aim to enable the formulation of standards. (authors)

  10. Bibliographical database of radiation biological dosimetry and risk assessment: Part 2

    International Nuclear Information System (INIS)

    Straume, T.; Ricker, Y.; Thut, M.

    1990-09-01

    This is part 11 of a database constructed to support research in radiation biological dosimetry and risk assessment. Relevant publications were identified through detailed searches of national and international electronic databases and through our personal knowledge of the subject. Publications were numbered and key worded, and referenced in an electronic data-retrieval system that permits quick access through computerized searches on authors, key words, title, year, journal name, or publication number. Photocopies of the publications contained in the database are maintained in a file that is numerically arranged by our publication acquisition numbers. This volume contains 1048 additional entries, which are listed in alphabetical order by author. The computer software used for the database is a simple but sophisticated relational database program that permits quick information access, high flexibility, and the creation of customized reports. This program is inexpensive and is commercially available for the Macintosh and the IBM PC. Although the database entries were made using a Macintosh computer, we have the capability to convert the files into the IBM PC version. As of this date, the database cites 2260 publications. Citations in the database are from 200 different scientific journals. There are also references to 80 books and published symposia, and 158 reports. Information relevant to radiation biological dosimetry and risk assessment is widely distributed within the scientific literature, although a few journals clearly predominate. The journals publishing the largest number of relevant papers are Health Physics, with a total of 242 citations in the database, and Mutation Research, with 185 citations. Other journals with over 100 citations in the database, are Radiation Research, with 136, and International Journal of Radiation Biology, with 132

  11. Continuum Modeling of Biological Network Formation

    KAUST Repository

    Albi, Giacomo; Burger, Martin; Haskovec, Jan; Markowich, Peter A.; Schlottbom, Matthias

    2017-01-01

    We present an overview of recent analytical and numerical results for the elliptic–parabolic system of partial differential equations proposed by Hu and Cai, which models the formation of biological transportation networks. The model describes

  12. Biological dosimetry after criticality accidents. Intercomparison exercise in the Silene Reactor - France

    International Nuclear Information System (INIS)

    Di Giorgio, Marina; Vallerga, Maria B.; Taja, Maria R.

    2004-01-01

    The Institute of Radiation Protection and Nuclear Safety Institute (IRSN) organized an international biological dosimetry intercomparison, at the SILENE experimental reactor (Valduc, France), simulating different criticality scenarios: bare source 4 Gy, lead shield source 1 and 2 Gy and gamma pure 60 Co source 2 Gy. Fifteen laboratories were involved in this exercise, including the Argentine Biological Dosimetry Laboratory. The purposes of the intercomparison were: 1) To compare the unstable chromosome aberration (UCA) frequency observed by the different laboratories; and 2) To compare the dose estimation for gamma rays and neutrons. The objects of the present work were: I) To compare the mean frequency of UCA observed by the Argentine laboratory with the mean frequency observed by the participant laboratories as a whole. II) To compare the dose estimates performed by the Argentine lab with those estimated by the other laboratories involved in the second stage of the intercomparison. Overall, the mean frequencies of UCA and the correspondent 95% confidence limits obtained by the Argentine lab were consistent with the results obtained by the laboratories as a whole. For the gamma pure scenario, smaller variations were observed among laboratories in terms of dose (CV=18,2%) than in terms of frequency (CV=30,1%). For the mixed field scenarios, only four laboratories, including the Argentine lab, estimated gamma and neutron components of the total dose and just two (Argentine lab and lab 12) were in agreement with the given physical doses. The 1 Gy experiment presented lesser variations both in terms of frequency and dose than the other two scenarios. For the 4 and 2 Gy experiments, variations in neutron dose were more significant than variations in gamma dose, related to the magnitude of the dose. The results suggest that intercomparison exercises jointly with the accreditation of biological dosimetry by cytogenetic service laboratories, in compliance with ISO

  13. Biological dosimetry of patients with differenced carcinoma of thyroid treated with Iodine-131

    International Nuclear Information System (INIS)

    Vallerga, M. B.; Rojo, A.M.; Taja, M.R.; Deluca, G.; Di Giorgio, M.; Fadel, A.; Cabrejas, M.; Valdivieso, C.

    2006-01-01

    The administration of I-131 to patient with Differentiated Thyroid Carcinoma (CaDiT) it is used inside the therapeutic outline as later step to the thyroidectomy. However, the good activity to give is of difficult determination due to factors such as, the variability in the capacity of tumoral reception of the I-131, distribution of the pharmaceutical, physiologic status, other associate pathologies, grade of advance of the illness, and previous treatments. Additionally, the activity to administer is dependent of the dose of tolerance in the healthy tissues; superior dose to 2 Gy in bone marrow, its could drive to myelotoxicity. At the moment, the form more extended of administration it is the empiric prescription that considers clinical parameters and of laboratory for their determination. Presently work, the protocol of applied treatment incorporates the evaluation for internal dosimetry and biological dosimetry to estimate absorbed dose in bone marrow. The biological estimate of the dose of these patients is based on the quantification of chromosomal aberrations whose frequency is referred to a curve-dose response in which the lymphocytes is irradiated in vitro with I-131, allowing to determine the in vivo dose to the patient's circulating lymphocytes. The objective of the present work is to determine the applicability of different cytogenetic essays in the estimate of the absorbed dose to the whole body or specific organs. Three patients were evaluated with CaDiT. Their treatment protocol consisted on a tracer administration of radioactive iodine of 74 - 111 MBq (2 - 3 mCi) and a therapy 7,4 - 11,1 GBq (200 - 300 mCi). Previous to the tracer administration and 8 days post-therapeutic administration took samples of veined blood that were evaluated by biological dosimetry by means of the application of the techniques: conventional cytogenetic Micronucleus and FISH (Hybridization in situ by Fluorescence). Starting from the frequencies of observed chromosomal

  14. Biological dosimetry in cases gives occupational high exposition to ionizing radiations

    International Nuclear Information System (INIS)

    Ramalho, Adriana T.; Costa, Maria Lucia P.; Oliveira, Monica S.; Silva, Francisco Cesar A.

    1998-01-01

    From 1983 the cytogenetics dosimetry method it has been used as routine in the IRD laboratory in the period 1983 at 1997 but a high exposition occupational case the physical dosimeters happened in Brazil they were investigated through the cytogenetics dosimetry technique. This technique is employ when the dosimetry personal marks a high dose to 100 mSv (0,1 Gy) that is the cut-off minimum detected in the dosimetry cytogenetics

  15. Calibration curves for biological dosimetry; Curvas de calibracion para dosimetria biologica

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero C, C.; Brena V, M. [ININ, A.P. 18-1027, 11801 Mexico D.F. (Mexico)]. E-mail cgc@nuclear.inin.mx

    2004-07-01

    The generated information by the investigations in different laboratories of the world, included the ININ, in which settles down that certain class of chromosomal leisure it increases in function of the dose and radiation type, has given by result the obtaining of calibrated curves that are applied in the well-known technique as biological dosimetry. In this work is presented a summary of the work made in the laboratory that includes the calibrated curves for gamma radiation of {sup 60} Cobalt and X rays of 250 k Vp, examples of presumed exposure to ionizing radiation, resolved by means of aberration analysis and the corresponding dose estimate through the equations of the respective curves and finally a comparison among the dose calculations in those people affected by the accident of Ciudad Juarez, carried out by the group of Oak Ridge, USA and those obtained in this laboratory. (Author)

  16. Dicentric chromosome aberration analysis using giemsa and centromere specific fluorescence in-situ hybridization for biological dosimetry: An inter- and intra-laboratory comparison in Indian laboratories

    International Nuclear Information System (INIS)

    Bhavani, M.; Tamizh Selvan, G.; Kaur, Harpreet; Adhikari, J.S.; Vijayalakshmi, J.; Venkatachalam, P.; Chaudhury, N.K.

    2014-01-01

    To facilitate efficient handling of large samples, an attempt towards networking of laboratories in India for biological dosimetry was carried out. Human peripheral blood samples were exposed to 60 Co γ-radiation for ten different doses (0–5 Gy) at a dose rate of 0.7 and 2 Gy/min. The chromosomal aberrations (CA) were scored in Giemsa-stained and fluorescence in-situ hybridization with centromere-specific probes. No significant difference (p>0.05) was observed in the CA yield for given doses except 4 and 5 Gy, between the laboratories, among the scorers and also staining methods adapted suggest the reliability and validates the inter-lab comparisons exercise for triage applications. - Highlights: • This is the first report from India on Networking for Biological Dosimetry preparedness using dicentric chromosomal (DC) aberration assay. • There is no significant difference in the in vitro dose response curve (Slope, Intercept, Curvature) constructed among the two labs. • No significant variation in the scoring of DC aberrations between the scorers irrespective of labs. • The DC results obtained by the labs from the Giemsa stained metaphase preparations were confirmed with centromere specific-FISH for further reliability and validity

  17. Analysis of MIR-18 results for physical and biological dosimetry: radiation shielding effectiveness in LEO

    International Nuclear Information System (INIS)

    Cucinotta, F.A.; Wilson, J.W.; Williams, J.R.; Dicello, J.F.

    2000-01-01

    We compare models of radiation transport and biological response to physical and biological dosimetry results from astronauts on the Mir space station. Transport models are shown to be in good agreement with physical measurements and indicate that the ratio of equivalent dose from the Galactic Cosmic Rays (GCR) to protons is about 3/2:1 and that this ratio will increase for exposures to internal organs. Two biological response models are used to compare to the Mir biodosimetry for chromosome aberration in lymphocyte cells; a track-structure model and the linear-quadratic model with linear energy transfer (LET) dependent weighting coefficients. These models are fit to in vitro data for aberration formation in human lymphocytes by photons and charged particles. Both models are found to be in reasonable agreement with data for aberrations in lymphocytes of Mir crew members: however there are differences between the use of LET dependent weighting factors and track structure models for assigning radiation quality factors. The major difference in the models is the increased effectiveness predicted by the track model for low charge and energy ions with LET near 10 keV/μm. The results of our calculations indicate that aluminum shielding, although providing important mitigation of the effects of trapped radiation, provides no protective effect from the galactic cosmic rays (GCR) in low-earth orbit (LEO) using either equivalent dose or the number of chromosome aberrations as a measure until about 100 g/cm 2 of material is used

  18. Analysis and assessment of the detriment in interventional radiology using biological dosimetry methods

    International Nuclear Information System (INIS)

    Montoro, A.; Almonacid, M.; Villaescusa, J.I.; Barquinero, J.F.; Rodriguez, P.; Barrios, L.; Verdu, G.; Ramos, M.

    2006-01-01

    Interventional radiologist and staff members usually are exposed to high levels of scattered radiation. As a result, the exposition to radiation procedures can produce detrimental effects that we would have to know. Effective dose is the quantity that better estimates the radiation risk. For this study we have realized an estimation of the radiological detriment to exposed workers of the Hospital la Fe de Valencia. For it, have been used physical doses registered in detectors T.L.D., and doses estimated by biological dosimetry in lymphocytes of peripheral blood. There has been estimated for every case the probability of effect of skin cancer and of non-solid cancers (leukaemia, lymphoma and myeloma), being compared with the baseline probability of natural effect. Biological doses were obtained by extrapolating the yield of dicentrics and translocations to their respective dose -effect curves. The discrepancies observed between physically recorded doses and biological estimated doses indicate that workers did not always wear their dosimeters or the dosimeters were not always in the radiation field. Cytogenetic studies should be extended to more workers to assess the risk derived from their occupational exposure. (authors)

  19. Analysis and assessment of the detriment in interventional radiology using biological dosimetry methods

    Energy Technology Data Exchange (ETDEWEB)

    Montoro, A.; Almonacid, M.; Villaescusa, J.I. [Hospital Univ. la Fe de Valen cian, Servicio de Proteccion Radiologica, Valencia (Spain); Barquinero, J.F.; Rodriguez, P. [Universitat Autonom a de Barcelona, Servicio de Dosimetria Biologica, Unidad de Antropologia, Departamento de Biologia Animal, Vegetal y Ecologia., Barcelona (Spain); Barrios, L. [Universidad Autonoma de Barcelona, Dept. de Biologia Celular y Fisiologia. Unidad de Biologia Celular, Barcelona (Spain); Verdu, G.; Ramos, M. [Universidad Politecnica de Valencia, Dept. de Ingenieria Quimica y Nuclear, Valencia, (Spain)

    2006-07-01

    Interventional radiologist and staff members usually are exposed to high levels of scattered radiation. As a result, the exposition to radiation procedures can produce detrimental effects that we would have to know. Effective dose is the quantity that better estimates the radiation risk. For this study we have realized an estimation of the radiological detriment to exposed workers of the Hospital la Fe de Valencia. For it, have been used physical doses registered in detectors T.L.D., and doses estimated by biological dosimetry in lymphocytes of peripheral blood. There has been estimated for every case the probability of effect of skin cancer and of non-solid cancers (leukaemia, lymphoma and myeloma), being compared with the baseline probability of natural effect. Biological doses were obtained by extrapolating the yield of dicentrics and translocations to their respective dose -effect curves. The discrepancies observed between physically recorded doses and biological estimated doses indicate that workers did not always wear their dosimeters or the dosimeters were not always in the radiation field. Cytogenetic studies should be extended to more workers to assess the risk derived from their occupational exposure. (authors)

  20. Network Analysis Tools: from biological networks to clusters and pathways.

    Science.gov (United States)

    Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Vanderstocken, Gilles; van Helden, Jacques

    2008-01-01

    Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.

  1. Characterizing the topology of probabilistic biological networks.

    Science.gov (United States)

    Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2013-01-01

    Biological interactions are often uncertain events, that may or may not take place with some probability. This uncertainty leads to a massive number of alternative interaction topologies for each such network. The existing studies analyze the degree distribution of biological networks by assuming that all the given interactions take place under all circumstances. This strong and often incorrect assumption can lead to misleading results. In this paper, we address this problem and develop a sound mathematical basis to characterize networks in the presence of uncertain interactions. Using our mathematical representation, we develop a method that can accurately describe the degree distribution of such networks. We also take one more step and extend our method to accurately compute the joint-degree distributions of node pairs connected by edges. The number of possible network topologies grows exponentially with the number of uncertain interactions. However, the mathematical model we develop allows us to compute these degree distributions in polynomial time in the number of interactions. Our method works quickly even for entire protein-protein interaction (PPI) networks. It also helps us find an adequate mathematical model using MLE. We perform a comparative study of node-degree and joint-degree distributions in two types of biological networks: the classical deterministic networks and the more flexible probabilistic networks. Our results confirm that power-law and log-normal models best describe degree distributions for both probabilistic and deterministic networks. Moreover, the inverse correlation of degrees of neighboring nodes shows that, in probabilistic networks, nodes with large number of interactions prefer to interact with those with small number of interactions more frequently than expected. We also show that probabilistic networks are more robust for node-degree distribution computation than the deterministic ones. all the data sets used, the software

  2. Recommendations to harmonize European early warning dosimetry network systems

    Science.gov (United States)

    Dombrowski, H.; Bleher, M.; De Cort, M.; Dabrowski, R.; Neumaier, S.; Stöhlker, U.

    2017-12-01

    After the Chernobyl nuclear power plant accident in 1986, followed by the Fukushima Nuclear power plant accident 25 years later, it became obvious that real-time information is required to quickly gain radiological information. As a consequence, the European countries established early warning network systems with the aim to provide an immediate warning in case of a major radiological emergency, to supply reliable information on area dose rates, contamination levels, radioactivity concentrations in air and finally to assess public exposure. This is relevant for governmental decisions on intervention measures in an emergency situation. Since different methods are used by national environmental monitoring systems to measure area dose rate values and activity concentrations, there are significant differences in the results provided by different countries. Because European and neighboring countries report area dose rate data to a central data base operated on behalf of the European Commission, the comparability of the data is crucial for its meaningful interpretation, especially in the case of a nuclear accident with transboundary implications. Only by harmonizing measuring methods and data evaluation, is the comparability of the dose rate data ensured. This publication concentrates on technical requirements and methods with the goal to effectively harmonize area dose rate monitoring data provided by automatic early warning network systems. The requirements and procedures laid down in this publication are based on studies within the MetroERM project, taking into account realistic technical approaches and tested procedures.

  3. Exploring biological network structure with clustered random networks

    Directory of Open Access Journals (Sweden)

    Bansal Shweta

    2009-12-01

    Full Text Available Abstract Background Complex biological systems are often modeled as networks of interacting units. Networks of biochemical interactions among proteins, epidemiological contacts among hosts, and trophic interactions in ecosystems, to name a few, have provided useful insights into the dynamical processes that shape and traverse these systems. The degrees of nodes (numbers of interactions and the extent of clustering (the tendency for a set of three nodes to be interconnected are two of many well-studied network properties that can fundamentally shape a system. Disentangling the interdependent effects of the various network properties, however, can be difficult. Simple network models can help us quantify the structure of empirical networked systems and understand the impact of various topological properties on dynamics. Results Here we develop and implement a new Markov chain simulation algorithm to generate simple, connected random graphs that have a specified degree sequence and level of clustering, but are random in all other respects. The implementation of the algorithm (ClustRNet: Clustered Random Networks provides the generation of random graphs optimized according to a local or global, and relative or absolute measure of clustering. We compare our algorithm to other similar methods and show that ours more successfully produces desired network characteristics. Finding appropriate null models is crucial in bioinformatics research, and is often difficult, particularly for biological networks. As we demonstrate, the networks generated by ClustRNet can serve as random controls when investigating the impacts of complex network features beyond the byproduct of degree and clustering in empirical networks. Conclusion ClustRNet generates ensembles of graphs of specified edge structure and clustering. These graphs allow for systematic study of the impacts of connectivity and redundancies on network function and dynamics. This process is a key step in

  4. Biological dosimetry in radiological protection: dose response curves elaboration for 60Co and 137Cs

    International Nuclear Information System (INIS)

    Silva, Marcia Augusta da

    1997-01-01

    Ionizing radiation sources for pacific uses are being extensively utilized by modern society and the applications of these sources have raised the probability of the occurrence of accidents. The accidental exposition to radiation creates a necessity of the development of methods to evaluate dose quantity. This data could be obtained by the measurement of damage caused by radiation in the exposed person. The radiation dose can be estimated in exposed persons through physical methods (physical dosimetry) but the biological methods can't be dispensed, and among them, the cytogenetic one that makes use of chromosome aberrations (dicentric and centric ring) formed in peripheral blood lymphocytes (PBL) exposed to ionizing radiation. This method correlates the frequency of radioinduced aberrations with the estimated absorbed dose, as in vitro as in vivo, which is called cytogenetic dosimetry. By the introduction of improved new techniques in culture, in the interpretation of aberrations in the different analysers of slides and by the adoption of different statistical programs to analyse the data, significant differences are observed among laboratories in dose-response curves (calibration curves). The estimation of absorbed dose utilizing other laboratory calibration curves may introduce some uncertainties, so the International Atomic Energy Agency (IAEA) advises that each laboratory elaborates your own dose-response curve for cytogenetic dosimetry. The results were obtained from peripheral blood lymphocytes of the healthy and no-smoking donors exposed to 60 Co and 137 Cs radiation, with dose rate of 5 cGy.min. -1 . Six points of dose were determined 20,50,100,200,300,400 cGy and the control not irradiated. The analysed aberrations were of chromosomic type, dicentric and centric ring. The dose response curve for dicentrics were obtained by frequencies weighted in liner-quadratic mathematic model and the equation resulted were for 60 Co: Y = (3 46 +- 2.14)10 -4 cGy -1 + (3

  5. Discriminative topological features reveal biological network mechanisms

    Directory of Open Access Journals (Sweden)

    Levovitz Chaya

    2004-11-01

    Full Text Available Abstract Background Recent genomic and bioinformatic advances have motivated the development of numerous network models intending to describe graphs of biological, technological, and sociological origin. In most cases the success of a model has been evaluated by how well it reproduces a few key features of the real-world data, such as degree distributions, mean geodesic lengths, and clustering coefficients. Often pairs of models can reproduce these features with indistinguishable fidelity despite being generated by vastly different mechanisms. In such cases, these few target features are insufficient to distinguish which of the different models best describes real world networks of interest; moreover, it is not clear a priori that any of the presently-existing algorithms for network generation offers a predictive description of the networks inspiring them. Results We present a method to assess systematically which of a set of proposed network generation algorithms gives the most accurate description of a given biological network. To derive discriminative classifiers, we construct a mapping from the set of all graphs to a high-dimensional (in principle infinite-dimensional "word space". This map defines an input space for classification schemes which allow us to state unambiguously which models are most descriptive of a given network of interest. Our training sets include networks generated from 17 models either drawn from the literature or introduced in this work. We show that different duplication-mutation schemes best describe the E. coli genetic network, the S. cerevisiae protein interaction network, and the C. elegans neuronal network, out of a set of network models including a linear preferential attachment model and a small-world model. Conclusions Our method is a first step towards systematizing network models and assessing their predictability, and we anticipate its usefulness for a number of communities.

  6. Reconstructing Causal Biological Networks through Active Learning.

    Directory of Open Access Journals (Sweden)

    Hyunghoon Cho

    Full Text Available Reverse-engineering of biological networks is a central problem in systems biology. The use of intervention data, such as gene knockouts or knockdowns, is typically used for teasing apart causal relationships among genes. Under time or resource constraints, one needs to carefully choose which intervention experiments to carry out. Previous approaches for selecting most informative interventions have largely been focused on discrete Bayesian networks. However, continuous Bayesian networks are of great practical interest, especially in the study of complex biological systems and their quantitative properties. In this work, we present an efficient, information-theoretic active learning algorithm for Gaussian Bayesian networks (GBNs, which serve as important models for gene regulatory networks. In addition to providing linear-algebraic insights unique to GBNs, leading to significant runtime improvements, we demonstrate the effectiveness of our method on data simulated with GBNs and the DREAM4 network inference challenge data sets. Our method generally leads to faster recovery of underlying network structure and faster convergence to final distribution of confidence scores over candidate graph structures using the full data, in comparison to random selection of intervention experiments.

  7. Radiation effects analysis in a group of interventional radiologists using biological and physical dosimetry methods

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, M., E-mail: WEMLmirapas@iqn.upv.e [Department of Chemical and Nuclear Engineering, Polytechnic University of Valencia, Camino de Vera s/n, 46022 Valencia (Spain); Montoro, A.; Almonacid, M. [Radiation Protection Service, Hospital Universitario La Fe Valencia (Spain); Ferrer, S. [Department of Chemical and Nuclear Engineering, Polytechnic University of Valencia, Camino de Vera s/n, 46022 Valencia (Spain); Barquinero, J.F. [Biological Dosimetry Service, Unit of Anthropology, Department of Animal and Vegetable Biology and Ecology, Universitat Autonoma de Barcelona (UAB) (Spain); Tortosa, R. [Radiation Protection Service, Hospital Universitario La Fe Valencia (Spain); Verdu, G. [Department of Chemical and Nuclear Engineering, Polytechnic University of Valencia, Camino de Vera s/n, 46022 Valencia (Spain); Rodriguez, P. [Biological Dosimetry Service, Unit of Anthropology, Department of Animal and Vegetable Biology and Ecology, Universitat Autonoma de Barcelona (UAB) (Spain); Barrios, L.L. [Department of Physiology and Cellular Biology, Unit of Cellular Biology (UAB) (Spain); Villaescusa, J.I. [Radiation Protection Service, Hospital Universitario La Fe Valencia (Spain)

    2010-08-15

    excess radio-induced risk of leukemia in the group under study. Finally, the maximum radiological detriment in the group, evaluated as the total number of radio-induced cancers using physical dosimetry, has been of 2.18/1000 person-year (skin and leukemia), and using biological dosimetry of 9.20/1000 PY (leukemia). As a conclusion, this study has provided an assessment of the non-deterministic effects (rate of radio-induced cancer incidence) attributable to the group under study due to their professional activity.

  8. Biological dosimetry in patients with differenced thyroid carcinoma treated with Iodine-131

    International Nuclear Information System (INIS)

    Vallerga, M.; Taja, Maria R.; Radl, A.; Rojo, Ana M.; Deluca, G.; Di Giogio, Marina; Fadel, A.; Chebel, G.; Oneto, A.; Cabrejas, Mariana

    2007-01-01

    The differentiated thyroid carcinoma (DTC), constitutes the 90 % of the thyroid gland cancers. 80% of patients are cured after the initial therapy and 12% remained disease-free after successive treatments. The 24 patients included in this study represent a sample of the aforementioned 12% and 8%, with recurrence in the first decade post-treatment (local disease and/or recurrence at distance). The internal radiotherapy with 131 I in patients with DTC is used within the therapeutic schema as a step post-thyroidectomy. The success of the therapy is to get a lethal dose in the tumor tissue, which depends on the therapeutic activity and the retention of 131 I, without exceeding the dose of tolerance in healthy tissues. The most widespread way of administration is the empirical prescription which considers the clinical and laboratory parameters for its determination. In this work, the treatment protocol applied incorporates assessment by biological (DB) and internal (DI) dosimetry for estimating absorbed dose to the whole body and bone marrow to manage a personalized therapeutic dose for each patient. The biological dose estimation is based on the quantification of chromosomal aberrations, which is often referred to a dose-response curve in which lymphocytes are irradiated in vitro with 131 I, allowing to determine the dose in vivo of circulating lymphocytes patients [es

  9. Biological dosimetry: the potential use of radiation-induced apoptosis in human T-lymphocytes

    International Nuclear Information System (INIS)

    Menz, R.; Andres, R.; Larsson, B.; Ozsahin, M.; Crompton, N.E.A.; Trott, K.

    1997-01-01

    An assay for biological dosimetry based on the induction of apoptosis in human T-lymphocytes is described. Radiation-induced apoptosis was assessed by flow cytometric identification of cells displaying apoptosis-associated DNA condensation. CD4 and CD8 T-lymphocytes were analysed. They were recognized on the basis of their cell-surface antigens. Four parameters were measured for both cell types: cell size, granularity, antigen immunofluorescence and DNA content. Apoptosis was quantified as the fraction of CD4-, or CD8-positive cells with a characteristic reduction of cell size and DNA content. At doses below 1 Gy, levels of radiation-induced apoptosis increased for up to 5 days after irradiation. Optimal dose discrimination was observed 4 days after irradiation, at which time the dose-response curves were linear, with a slope of 8% ± 0.5% per 0.1 Gy. In controlled, dose-response experiments the lowest dose level at which the radiation-induced apoptosis frequency was still significantly above control was 0.05 Gy. After 5 days post-irradiation incubation, intra- and interdonor variations were measured and found to be similar; thus, apoptotic levels depend more on the dose than on the donor. The results demonstrate the potential of this assay as a biological dosimeter. (orig.)

  10. Challenges of analysing suspected over exposed subjects using biological dosimetry at Sri Ramachandra University

    International Nuclear Information System (INIS)

    Vijayalakshimi, J.; Venkatachalam, P.; Solomon, F.D. Paul

    2016-01-01

    Biological dosimetry based on the analysis of dicentric chromosomes has become a routine component of the radiological protection programmes and has a valuable role to contribute in suspected over exposed subjects who perform diagnostic and therapeutic procedures. The Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, has been involved in the standardization of chromosomal aberration analysis as a biological dosimeter for investigating accidental ionising radiation exposure since 1998. Our laboratory has been accredited since 2007 by Atomic Energy Regulatory Board. The initial process was to establish the in vitro dose response curve for various type of low LET ionizing radiation. Since accreditation, a total of 61 subjects have been referred to Sri Ramachandra University from SRRC, Kalpakkam. Brief social/medical history and informed consent are being obtained prior to blood samplings. The dose estimates expressed in sievert (Sv) measured by Thermoluminescence badges was in the range of 0.05-2779.05 mSv. Chromosomal aberration assay was used for analysis which allows direct detection of aberration in peripheral blood lymphocytes. The test was performed as per the standard operating protocol on peripheral blood lymphocyte. Currently the dose response curve for the automated scoring process in under way and we hope to improve upon quality and turnaround time using the automation available. Future challenge would be to establish an in vitro dose response curve with automated scoring technique and developing inter-laboratory comparison of dose response generated using automation

  11. Preliminary study on biological dosimetry using alkaline single cell gel electrophoresis of human peripheral lymphocytes

    International Nuclear Information System (INIS)

    Liu Qingjie; Lu Xue; Feng Jiangbing; Chen Deqing; Chen Xiaosui

    2006-01-01

    Objective: To explore the feasibility of alkaline single cell gel electrophoresis (SCGE) in biological dosimetry of ionizing radiation. Methods: Normal peripheral blood samples from two healthy males were exposed to different doses coblat-60 gamma-rays, ranged from 0 to 5 Gy, and the tail length (TL) and Oliver tail moment (TM) of the lymphocytes were analyzed with SCGE. The dose-effect curves of TL and TM were fitted respectively. The TL and TM of lymphocytes for eight radiation workers were analyzed with SCGE, cumulative doses were estimated using the fitted TL and TM equations, and then compared with the recorded monitoring doses. Results: The TLs or TMs of normal human lymphocytes were increased with the irradiation doses, and its relationship can be fitted with a linear-quadratic equations: Y=13.59 + 20.87X - 2.27 X 2 for TL, and Y = 8.50 + 15.04X - 1.43X 2 for TM, respectively (Y denotes TL or TM value, X is radiation dose). The doses estimated with TM equation were closer to the recorded monitoring doses than that with TL equation. Conclusions: The TM in lymphocytes analyzed with SCGE is a promising radiation biological dosimeter. (authors)

  12. Use of FISH-translocations analyses for retrospective biological dosimetry: How stable are stable chromosome aberrations?

    International Nuclear Information System (INIS)

    Darroudi, F.

    2000-01-01

    Chromosome aberrations, in particular dicentrics, in peripheral blood lymphocytes are used to estimate the absorbed dose immediately following a radiation accident. However, difficulties for dose estimation arise with old exposures, due to a decline of cells containing unstable dicentric aberrations. The fluorescence in situ hybridisation (FISH) technique employing chromosome specific DNA libraries to 'paint' individual human chromosomes has opened new perspectives for rapid and reliable detection of stable chromosome aberrations such as translocations. The inherent stability of translocations over cell generations has enabled them to be used as a biodosemeter. However, due to the limited life of circulating T-lymphocytes, a level of uncertainty exists on the long-term persistence of stable translocations. The objectives of the present work are to present the current state of knowledge on the stability of translocations detected by FISH. The following aspects have been considered; (1) experience so far of retrospective biological dosimetry in humans following accidental and occupational over-exposure, (2) animal studies using mice and monkeys, (3) the influence of subsequent cell divisions on the yield and persistence of translocations following in vitro irradiation of human lymphocytes, and (4) the needs for further work to standardise and validate the use of FISH as a biological dosemeter, and to investigate the influence of various parameters such as radiation quality, dose rate and the discrimination of sub-types of translocations on persistence. (author)

  13. Biological and Environmental Research Network Requirements

    Energy Technology Data Exchange (ETDEWEB)

    Balaji, V. [Princeton Univ., NJ (United States). Earth Science Grid Federation (ESGF); Boden, Tom [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Cowley, Dave [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dart, Eli [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Dattoria, Vince [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Desai, Narayan [Argonne National Lab. (ANL), Argonne, IL (United States); Egan, Rob [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Foster, Ian [Argonne National Lab. (ANL), Argonne, IL (United States); Goldstone, Robin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gregurick, Susan [U.S. Dept. of Energy, Washington, DC (United States). Biological Systems Science Division; Houghton, John [U.S. Dept. of Energy, Washington, DC (United States). Biological and Environmental Research (BER) Program; Izaurralde, Cesar [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Johnston, Bill [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Joseph, Renu [U.S. Dept. of Energy, Washington, DC (United States). Climate and Environmental Sciences Division; Kleese-van Dam, Kerstin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lipton, Mary [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Monga, Inder [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Pritchard, Matt [British Atmospheric Data Centre (BADC), Oxon (United Kingdom); Rotman, Lauren [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Strand, Gary [National Center for Atmospheric Research (NCAR), Boulder, CO (United States); Stuart, Cory [Argonne National Lab. (ANL), Argonne, IL (United States); Tatusova, Tatiana [National Inst. of Health (NIH), Bethesda, MD (United States); Tierney, Brian [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Thomas, Brian [Univ. of California, Berkeley, CA (United States); Williams, Dean N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Zurawski, Jason [Internet2, Washington, DC (United States)

    2013-09-01

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy (DOE) Office of Science (SC), the single largest supporter of basic research in the physical sciences in the United States. In support of SC programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet be a highly successful enabler of scientific discovery for over 25 years. In November 2012, ESnet and the Office of Biological and Environmental Research (BER) of the DOE SC organized a review to characterize the networking requirements of the programs funded by the BER program office. Several key findings resulted from the review. Among them: 1) The scale of data sets available to science collaborations continues to increase exponentially. This has broad impact, both on the network and on the computational and storage systems connected to the network. 2) Many science collaborations require assistance to cope with the systems and network engineering challenges inherent in managing the rapid growth in data scale. 3) Several science domains operate distributed facilities that rely on high-performance networking for success. Key examples illustrated in this report include the Earth System Grid Federation (ESGF) and the Systems Biology Knowledgebase (KBase). This report expands on these points, and addresses others as well. The report contains a findings section as well as the text of the case studies discussed at the review.

  14. Solid State and Chemical Radiation Dosimetry in Medicine and Biology. Proceedings of a Symposium

    International Nuclear Information System (INIS)

    1967-01-01

    Proceedings of a Symposium organized by the IAEA and held in Vienna, 3-7 October 1966. The meeting was attended by 104 participants from 21 countries and three international organizations. Contents: Solid state dosimetry (17 papers); Chemical dosimetry (10 papers); Invited lectures (2 papers); General aspects and other methods of dosimetry (6 papers); Panel discussion on research and development needed in dosimetry. Each paper is in its original language (32 English, 2 French and 1 Spanish) and is preceded by an abstract in English and one in the original language, if this is not English. Discussions are in English. (author)

  15. Solid State and Chemical Radiation Dosimetry in Medicine and Biology. Proceedings of a Symposium

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1967-03-15

    Proceedings of a Symposium organized by the IAEA and held in Vienna, 3-7 October 1966. The meeting was attended by 104 participants from 21 countries and three international organizations. Contents: Solid state dosimetry (17 papers); Chemical dosimetry (10 papers); Invited lectures (2 papers); General aspects and other methods of dosimetry (6 papers); Panel discussion on research and development needed in dosimetry. Each paper is in its original language (32 English, 2 French and 1 Spanish) and is preceded by an abstract in English and one in the original language, if this is not English. Discussions are in English. (author)

  16. Biological Dosimetry of In Vitro Irradiation with Radionuclides : Comparison of Whole Blood, Lymphocyte and Buffy Coat Culture

    International Nuclear Information System (INIS)

    Kim, Jong Ho; Lee, Dong Soo; Choi, Chang Woon; Chung, June Key; Lee, Myung Chul; Koh, Chang Soon; Kim, Chong Soon; Kim, Hee Geun; Kang, Duck Won; Song, Myung Jae

    1995-01-01

    The purpose of this study was to establish mononuclear cell cultures such as lymphocytes or buffy coat for the biological dosimetry of in vitro irradiation of the radionuclide Tc-99m in order to exclude the effect of residual doses seen in the cultures of whole blood. Biological dosimetry of Tc-99m on cultured mononuclear cells at doses ranging from 0.05 to 6.00 Gy, by scoring unstable chromosomal aberrations(Ydr) observed in cultured lymphocytes, were performed using peripheral venous blood of healthy normal person. The results showed that; (1) In vitro irradiation of radioisotope in separated lymphocyte or buffy coat showed trace amount af residual doses of isotope after washing. Residual doses of isotopes are increased in proportion tn exposed time and irradiated dose without difference between I-131 anct Tc-99m. (2) We obtained these linear-quadratic dose response equations in lymphocyte and buffy coat culture after in vitro irradiation of Tc-99m, respectively (Ydr = 0,001949 D 2 +0,006279D+ 0.000185; Ydr= 0.002531 D 2 -0.003274 D+0.003488). In conclusion, the linear quadrstic dose response equation from in vitro irradiation of Tc-99m with lymphocyte and buffy coat culture was thought to be useful for assessing Tc-99m indueed biological effects. And mononuclear cell cultures seem to be the most appropriate experimental model for the assessment of biological dosimetry of internal irradiation of radionuclides.

  17. 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.

  18. Dense module enumeration in biological networks

    Science.gov (United States)

    Tsuda, Koji; Georgii, Elisabeth

    2009-12-01

    Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

  19. Dense module enumeration in biological networks

    International Nuclear Information System (INIS)

    Tsuda, Koji; Georgii, Elisabeth

    2009-01-01

    Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

  20. Supporting Treatment Decisions in Patients with Differentiated Thyroid Carcinoma (DTC) under Radioiodine-131 Therapy: Role of Biological Dosimetry Assessment

    International Nuclear Information System (INIS)

    Fadel, A.M.; Chebel, G.M.; Di Giorgio, M.; Vallerga, M.B.; Taja, M.R.; Radl, A.; Bubniak, R.V.; Oneto, A.

    2010-01-01

    Radioiodine-131 therapy is applied in patients with differentiated thyroid carcinoma (DTC), within the therapeutic scheme following thyroidectomy, for the ablation of thyroid remnants and treatment of metastatic disease. Several approaches for the selection of a therapeutic dose were applied. The aim of this therapy is to achieve a lethal dose in the tumor tissue, without exceeding the dose of tolerance in healthy tissues (doses greater than 2 Gy in bone marrow could lead to myelotoxicity). In this work, the treatment protocol used incorporates the assessment by biological dosimetry (BD) for estimating doses to whole body and bone marrow, to tailor patient's treatment. Biological Dosimetry prospective studies conducted on samples from patients with cumulative activities, before and after each therapeutic administration, allows to evaluate DNA damage and repair capacity in peripheral blood lymphocytes. (authors)

  1. The use of apoptosis in human lymphocytes peripheral as alternative methods in biological dosimetry of radiation effects from cobalt-60

    International Nuclear Information System (INIS)

    Lemes, Marisa

    1997-01-01

    Gamma rays affect cells in dose-response manner, resulting in cell death, as in cancer radiotherapy. The ionizing radiation acts by transferring energy, mainly by free radicals from water radiolysis that result in nucleic acid damage and other effects in lipids and proteins, The level of exposure is indirectly estimated by physical dosimetry, but the biological dosimetry can measure the direct radiation effect, mainly in post-dividing cells by classical cytogenetic approach. Recently, it was reported that irradiated cells develop an induced programmed death or apoptosis. With a biological dosimetric technique, we measured apoptotic cell fraction in 60 Co in vitro irradiated blood cells from voluntary healthy donors. The agarose gel electrophoresis showed a low sensitivity, because cell DNA presented the characteristic pattern only when the cells were exposed to 100 c Gy or more. Using a terminal DNA labeling technique we observed that the apoptotic cell fraction proportionally increases with irradiation. Similar sensitivity was observed when compared to classical cytogenetics (3 c Gy minimum detection level). These techniques are easier to perform, do not need cell culture and all cells, including interphase ones, can be analyzed, providing a good tool in biological dosimetry. (author)

  2. Characterizing Topology of Probabilistic Biological Networks.

    Science.gov (United States)

    Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2013-09-06

    Biological interactions are often uncertain events, that may or may not take place with some probability. Existing studies analyze the degree distribution of biological networks by assuming that all the given interactions take place under all circumstances. This strong and often incorrect assumption can lead to misleading results. Here, we address this problem and develop a sound mathematical basis to characterize networks in the presence of uncertain interactions. We develop a method that accurately describes the degree distribution of such networks. We also extend our method to accurately compute the joint degree distributions of node pairs connected by edges. The number of possible network topologies grows exponentially with the number of uncertain interactions. However, the mathematical model we develop allows us to compute these degree distributions in polynomial time in the number of interactions. It also helps us find an adequate mathematical model using maximum likelihood estimation. Our results demonstrate that power law and log-normal models best describe degree distributions for probabilistic networks. The inverse correlation of degrees of neighboring nodes shows that, in probabilistic networks, nodes with large number of interactions prefer to interact with those with small number of interactions more frequently than expected.

  3. Activities developed by the biological dosimetry laboratory of the Autoridad Regulatoria Nuclear - ARN of Argentina; Actividades desarrolladas por el laboratorio de dosimetria biologica de la Autoridad Regulatoria Nuclear de Argentina

    Energy Technology Data Exchange (ETDEWEB)

    Radl, A.; Sapienza, C. E.; Taja, M. R.; Bubniak, R.; Deminge, M.; Di Giorgio, M., E-mail: csapienza@arn.gob.ar [Autoridad Regulatoria Nuclear (ARN), Buenos Aires (Argentina)

    2013-07-01

    Biological dosimetry (DB) allows to estimate doses absorbed in individuals exposed to ionizing radiation through the quantification of stable and unstable chromosome aberrations (SCA and UCA). The frequency of these aberrations is referred to a calibration dose response curve (in vitro) to determine the doses of the individual to the whole body. The DB is a necessary support for programs of national radiation protection and response systems in nuclear or radiological emergencies in the event of accidental or incidental, single overexposure or large scale. In this context the Laboratory of Dosimetry Biological (LDB) of the Authority Regulatory Nuclear (ARN) Argentina develops and applies different dosimeters cytogenetic from four decades ago. These dosimeters provide a fact more within the whole of the information necessary for an accidental, complementing the physical and clinical dosimetry exposure assessment. The most widely used in the DB biodosimetric method is the quantification of SCA (dicentrics and rings Central) from a sample of venous blood. The LDB is accredited for the trial, under rules IRAM 301: 2005 (ISO / IEC 17025: 2005) and ISO 19238:2004. Test applies to the immediate dosimetry evaluation of acute exposures, all or a large part of the body in the range 0,1-5 Gy. In this context the LDB is part of the Latin American network of DB (LBDNet), BioDoseNet-who and response system in radiological emergencies and nuclear IAEA-RANET, being enabled to summon the LBDNet if necessary.

  4. Review of Biological Network Data and Its Applications

    Directory of Open Access Journals (Sweden)

    Donghyeon Yu

    2013-12-01

    Full Text Available Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

  5. Neutron dosimetry - A review

    Energy Technology Data Exchange (ETDEWEB)

    Baum, J W

    1955-03-29

    This review summarizes information on the following subjects: (1) physical processes of importance in neutron dosimetry; (2) biological effects of neutrons; (3) neutron sources; and (4) instruments and methods used in neutron dosimetry. Also, possible improvements in dosimetry instrumentation are outlined and discussed. (author)

  6. A contribution to the study of the biological dosimetry in clinical radiopathology

    International Nuclear Information System (INIS)

    Eston, T.E. de.

    1983-01-01

    The effects of total body irradiation with different radiation doses from a 4MeV linear accelerator on organs and tissues of adult male rabbits were studied. Doses of 0.50, 2.00, 6.00 and 8.00 Gy were applied. Different organic parameters were evaluated before and after various periods of the post-irradiation time. Mortality did not occured for 0.50 or 2.00 Gy, but morbility was greater in comparison with the control; sexual potency was maintained. 'Impotentia colundi' occured with 6 Gy. A small loss of weight occured with 2.00 Gy and a higher loss for 6.00 Gy, with later recovery. Blood parameters varied even for lowest dose. Alterations were evident in the bone marrow activity for 2.00 and 6.00 Gy. Spermatides, spermatocytes and mature spermatozoids were affect even by low doses, the laters loosing motility. Significant difference was observed in the relation DNA/RNA for irradiated-and control animals. The results showed that T3 asssay could serve as 'biological indicator' of irradiation in a period of at least 7 hours and for doses of 4Gy or more. Using the kinetic method, an increase of glutamic oxalacetic transaminase (GOT) seric levels was observed for 6.00 Gy after 7 hours and a decrease for the glutamic pyruvic transaminase (GPT). Fasting glycemy and catecolamines urinary extraction were not statiscally significants. The study of chromosomal aberrations that occur in lymphocytes after 'in vitro' irradiation showed that this is at the present moment the most efficient method for biological dosimetry. (M.A.) [pt

  7. Functional model of biological neural networks.

    Science.gov (United States)

    Lo, James Ting-Ho

    2010-12-01

    A functional model of biological neural networks, called temporal hierarchical probabilistic associative memory (THPAM), is proposed in this paper. THPAM comprises functional models of dendritic trees for encoding inputs to neurons, a first type of neuron for generating spike trains, a second type of neuron for generating graded signals to modulate neurons of the first type, supervised and unsupervised Hebbian learning mechanisms for easy learning and retrieving, an arrangement of dendritic trees for maximizing generalization, hardwiring for rotation-translation-scaling invariance, and feedback connections with different delay durations for neurons to make full use of present and past informations generated by neurons in the same and higher layers. These functional models and their processing operations have many functions of biological neural networks that have not been achieved by other models in the open literature and provide logically coherent answers to many long-standing neuroscientific questions. However, biological justifications of these functional models and their processing operations are required for THPAM to qualify as a macroscopic model (or low-order approximate) of biological neural networks.

  8. Network biology concepts in complex disease comorbidities

    DEFF Research Database (Denmark)

    Hu, Jessica Xin; Thomas, Cecilia Engel; Brunak, Søren

    2016-01-01

    collected electronically, disease co-occurrences are starting to be quantitatively characterized. Linking network dynamics to the real-life, non-ideal patient in whom diseases co-occur and interact provides a valuable basis for generating hypotheses on molecular disease mechanisms, and provides knowledge......The co-occurrence of diseases can inform the underlying network biology of shared and multifunctional genes and pathways. In addition, comorbidities help to elucidate the effects of external exposures, such as diet, lifestyle and patient care. With worldwide health transaction data now often being...

  9. Social traits, social networks and evolutionary biology.

    Science.gov (United States)

    Fisher, D N; McAdam, A G

    2017-12-01

    effects) provides the potential to understand how entire networks of social interactions in populations influence phenotypes and predict how these traits may evolve. By theoretical integration of social network analysis and quantitative genetics, we hope to identify areas of compatibility and incompatibility and to direct research efforts towards the most promising areas. Continuing this synthesis could provide important insights into the evolution of traits expressed in a social context and the evolutionary consequences of complex and nuanced social phenotypes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  10. Biological in vivo dosimetry with an external measuring technique under application of a labelled DNA-precursor (iodine-125-desoxyuridine)

    International Nuclear Information System (INIS)

    Porschen, W.; Zamboglou, N.; Muehlensiepen, H.; Feinendegen, L.E.

    1976-01-01

    The depression of the incorporation rate of IDU in the whole body or in the bone marrow is a sensitive indicator for a whole-body irradiation. It was found that the maximum effect is observed some 4 hours after irradiation. For this reason, bone marrow cells were labelled in vitro with IDU 4 hours after whole-body irradiation. This method proved to be extraordinarily sensitive and resulted in reproducible effects which occurred already at doses below 5 rad. All the other biological methods of dosimetry known so far are less sensitive. Although the theory explaining these results is not yet fully clarified, this method of dosimetry appears to offer practical possibilities of application. (orig.) [de

  11. Novel topological descriptors for analyzing biological networks

    Directory of Open Access Journals (Sweden)

    Varmuza Kurt K

    2010-06-01

    Full Text Available Abstract Background Topological descriptors, other graph measures, and in a broader sense, graph-theoretical methods, have been proven as powerful tools to perform biological network analysis. However, the majority of the developed descriptors and graph-theoretical methods does not have the ability to take vertex- and edge-labels into account, e.g., atom- and bond-types when considering molecular graphs. Indeed, this feature is important to characterize biological networks more meaningfully instead of only considering pure topological information. Results In this paper, we put the emphasis on analyzing a special type of biological networks, namely bio-chemical structures. First, we derive entropic measures to calculate the information content of vertex- and edge-labeled graphs and investigate some useful properties thereof. Second, we apply the mentioned measures combined with other well-known descriptors to supervised machine learning methods for predicting Ames mutagenicity. Moreover, we investigate the influence of our topological descriptors - measures for only unlabeled vs. measures for labeled graphs - on the prediction performance of the underlying graph classification problem. Conclusions Our study demonstrates that the application of entropic measures to molecules representing graphs is useful to characterize such structures meaningfully. For instance, we have found that if one extends the measures for determining the structural information content of unlabeled graphs to labeled graphs, the uniqueness of the resulting indices is higher. Because measures to structurally characterize labeled graphs are clearly underrepresented so far, the further development of such methods might be valuable and fruitful for solving problems within biological network analysis.

  12. Bayesian Network Webserver: a comprehensive tool for biological network modeling.

    Science.gov (United States)

    Ziebarth, Jesse D; Bhattacharya, Anindya; Cui, Yan

    2013-11-01

    The Bayesian Network Webserver (BNW) is a platform for comprehensive network modeling of systems genetics and other biological datasets. It allows users to quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data and use the model to understand relationships between network variables. Many datasets, including those used to create genetic network models, contain both discrete (e.g. genotype) and continuous (e.g. gene expression traits) variables, and BNW allows for modeling hybrid datasets. Users of BNW can incorporate prior knowledge during structure learning through an easy-to-use structural constraint interface. After structure learning, users are immediately presented with an interactive network model, which can be used to make testable hypotheses about network relationships. BNW, including a downloadable structure learning package, is available at http://compbio.uthsc.edu/BNW. (The BNW interface for adding structural constraints uses HTML5 features that are not supported by current version of Internet Explorer. We suggest using other browsers (e.g. Google Chrome or Mozilla Firefox) when accessing BNW). ycui2@uthsc.edu. Supplementary data are available at Bioinformatics online.

  13. Continuum Modeling of Biological Network Formation

    KAUST Repository

    Albi, Giacomo

    2017-04-10

    We present an overview of recent analytical and numerical results for the elliptic–parabolic system of partial differential equations proposed by Hu and Cai, which models the formation of biological transportation networks. The model describes the pressure field using a Darcy type equation and the dynamics of the conductance network under pressure force effects. Randomness in the material structure is represented by a linear diffusion term and conductance relaxation by an algebraic decay term. We first introduce micro- and mesoscopic models and show how they are connected to the macroscopic PDE system. Then, we provide an overview of analytical results for the PDE model, focusing mainly on the existence of weak and mild solutions and analysis of the steady states. The analytical part is complemented by extensive numerical simulations. We propose a discretization based on finite elements and study the qualitative properties of network structures for various parameter values.

  14. Light scattering by irradiated cells as a method of biological dosimetry

    International Nuclear Information System (INIS)

    Ostashevsky, J.

    1984-01-01

    Light scattering (LS) parameters between 350-500 nm wavelength have been studied for 2 groups of cells: 1) blood (BL) and thymus (TL) lymphocytes of rats and mice, and 2) Ehrlich ascite tumor (EAT) cells. LS measurements of freshly prepared cell suspensions have been made 24 hrs after x-ray irradiation of rodents (250 Kev, HVL = 2 mm Cu) at doses of 50-900 cGy. A steep (30% per Gy) linear (50-800 cGy for TL and 50-400 cGy for BL) dose-dependence was obtained for the increase in 90 0 -angle LS intensity. Increase in absorption (low-angle LS) was also linear (50-800 cGy for TL and BL) but less steep (9% per Gy). Irradiated cells were the same size as unirradiated. Changes in LS for TL and BL appear to follow the appearance of additional vacuoles which may become new internal smaller-size centers of LS. This suggestion is supported by direct observations of cells with dark-field microscopy. For EAT cells, both 90 0 and low angle LS had the same slope. This slope (4% per Gy) is much shallower than that for BL and TL, and quantitatively coincides with enlargement of area of EAT cells, which could explain LS changes. The difference in LS behavior of the two cellular groups reflects a difference in their early response to irradiation: interphase death for TL and BL, vs division delay for EAT cells. The above data suggest the fast and simple method of biological dosimetry

  15. The Relevance of Chromosome Aberration Yields for Biological Dosimetry After Low-Level Occupational Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Bauchinger, M.; Schmid, E.; Hug, O. [Gesellschaft fuer Strahlenforschung, Institut fuer Biologie, Neuherberg, Federal Republic of Germany (Germany); Strahlenbiologisches Institut der Universitaet Muenchen, Federal Republic of Germany (Germany)

    1971-06-15

    The usefulness of chromosome analysis for biological dosimetry has been tested in two groups of persons occupationally exposed to radiation: (I) in nurses employed in gynaecological radiology, exposed especially when handling radium inserts; and (II) in nuclear industry workers, all of which were exposed to external gamma irradiation and some of them also to internal radiation after incorporation of various radionuclides. The total dose registered with personal dosimeters ranged in Group 1 from 0.1 to 91.1 rem accumulated over working periods of 0.1 to 13 years, and in Group II from 1.0 to 18.2 rem accumulated over 1 to 9 years. Compared with unexposed controls, both groups exhibit a significant increase of cells with chromosome aberrations as well as larger numbers of breaks per cell. Dicentrics and rings could be observed in some cells, providing good evidence for previous radiation exposure, since these types of aberrations are extremely rare events in unexposed individuals. No correlation between the aberration yields and the film badge values could be demonstrated in Group II. Also, in Group I the fluctuations from individual to individual are rather high. Nevertheless, a positive correlation to the ''dose'' was obtained. Even a sub-group of the nurses that had only been exposed to 20 rem showed significantly more aberrations than control persons. From the results obtained, type and frequency of chromosome aberrations may be considered an indicator of radiation exposure even at the low doses. The reasons for lack of correspondence of chromosome aberration yields and the results of personal monitoring procedures are discussed in detail. (author)

  16. Computing chemical organizations in biological networks.

    Science.gov (United States)

    Centler, Florian; Kaleta, Christoph; di Fenizio, Pietro Speroni; Dittrich, Peter

    2008-07-15

    Novel techniques are required to analyze computational models of intracellular processes as they increase steadily in size and complexity. The theory of chemical organizations has recently been introduced as such a technique that links the topology of biochemical reaction network models to their dynamical repertoire. The network is decomposed into algebraically closed and self-maintaining subnetworks called organizations. They form a hierarchy representing all feasible system states including all steady states. We present three algorithms to compute the hierarchy of organizations for network models provided in SBML format. Two of them compute the complete organization hierarchy, while the third one uses heuristics to obtain a subset of all organizations for large models. While the constructive approach computes the hierarchy starting from the smallest organization in a bottom-up fashion, the flux-based approach employs self-maintaining flux distributions to determine organizations. A runtime comparison on 16 different network models of natural systems showed that none of the two exhaustive algorithms is superior in all cases. Studying a 'genome-scale' network model with 762 species and 1193 reactions, we demonstrate how the organization hierarchy helps to uncover the model structure and allows to evaluate the model's quality, for example by detecting components and subsystems of the model whose maintenance is not explained by the model. All data and a Java implementation that plugs into the Systems Biology Workbench is available from http://www.minet.uni-jena.de/csb/prj/ot/tools.

  17. Biological dosimetry of ionizing radiation: Evaluation of the dose with cytogenetic methodologies by the construction of calibration curves

    Science.gov (United States)

    Zafiropoulos, Demetre; Facco, E.; Sarchiapone, Lucia

    2016-09-01

    In case of a radiation accident, it is well known that in the absence of physical dosimetry biological dosimetry based on cytogenetic methods is a unique tool to estimate individual absorbed dose. Moreover, even when physical dosimetry indicates an overexposure, scoring chromosome aberrations (dicentrics and rings) in human peripheral blood lymphocytes (PBLs) at metaphase is presently the most widely used method to confirm dose assessment. The analysis of dicentrics and rings in PBLs after Giemsa staining of metaphase cells is considered the most valid assay for radiation injury. This work shows that applying the fluorescence in situ hybridization (FISH) technique, using telomeric/centromeric peptide nucleic acid (PNA) probes in metaphase chromosomes for radiation dosimetry, could become a fast scoring, reliable and precise method for biological dosimetry after accidental radiation exposures. In both in vitro methods described above, lymphocyte stimulation is needed, and this limits the application in radiation emergency medicine where speed is considered to be a high priority. Using premature chromosome condensation (PCC), irradiated human PBLs (non-stimulated) were fused with mitotic CHO cells, and the yield of excess PCC fragments in Giemsa stained cells was scored. To score dicentrics and rings under PCC conditions, the necessary centromere and telomere detection of the chromosomes was obtained using FISH and specific PNA probes. Of course, a prerequisite for dose assessment in all cases is a dose-effect calibration curve. This work illustrates the various methods used; dose response calibration curves, with 95% confidence limits used to estimate dose uncertainties, have been constructed for conventional metaphase analysis and FISH. We also compare the dose-response curve constructed after scoring of dicentrics and rings using PCC combined with FISH and PNA probes. Also reported are dose response curves showing scored dicentrics and rings per cell, combining

  18. Learning and coding in biological neural networks

    Science.gov (United States)

    Fiete, Ila Rani

    How can large groups of neurons that locally modify their activities learn to collectively perform a desired task? Do studies of learning in small networks tell us anything about learning in the fantastically large collection of neurons that make up a vertebrate brain? What factors do neurons optimize by encoding sensory inputs or motor commands in the way they do? In this thesis I present a collection of four theoretical works: each of the projects was motivated by specific constraints and complexities of biological neural networks, as revealed by experimental studies; together, they aim to partially address some of the central questions of neuroscience posed above. We first study the role of sparse neural activity, as seen in the coding of sequential commands in a premotor area responsible for birdsong. We show that the sparse coding of temporal sequences in the songbird brain can, in a network where the feedforward plastic weights must translate the sparse sequential code into a time-varying muscle code, facilitate learning by minimizing synaptic interference. Next, we propose a biologically plausible synaptic plasticity rule that can perform goal-directed learning in recurrent networks of voltage-based spiking neurons that interact through conductances. Learning is based on the correlation of noisy local activity with a global reward signal; we prove that this rule performs stochastic gradient ascent on the reward. Thus, if the reward signal quantifies network performance on some desired task, the plasticity rule provably drives goal-directed learning in the network. To assess the convergence properties of the learning rule, we compare it with a known example of learning in the brain. Song-learning in finches is a clear example of a learned behavior, with detailed available neurophysiological data. With our learning rule, we train an anatomically accurate model birdsong network that drives a sound source to mimic an actual zebrafinch song. Simulation and

  19. Collaborative Physical and Biological Dosimetry Studies for Neutron Capture Therapy at the RA-1 Research Reactor Facility

    Energy Technology Data Exchange (ETDEWEB)

    David W. Nigg; Amanda E. Schwint; John K. Hartwell; Elisa M. Heber; Veronica Trivillin; Jorge Castillo; Luis Wentzeis; Patrick Sloan; Charles A. Wemple

    2004-10-01

    Initial physical dosimetry measurements have been completed using activation spectrometry and thermoluminiscent dosimeters to characterize the BNCT irradiation facility developed at the RA-1 research reactor operated by the Argentine National Atomic Energy Commission in Buenos Aires. Some biological scoping irradiations have also been completed using a small-animal (hamster) oral mucosa tumor model. Results indicate that the RA-1 neutron source produces useful dose rates but that some improvements in the initial configuration will be needed to optimize the spectrum for thermal-neutron BNCT research applications.

  20. Collaborative Physical and Biological Dosimetry Studies for Neutron Capture Therapy at the RA-1 Research Reactor Facility

    Energy Technology Data Exchange (ETDEWEB)

    Nigg, D.W.; Schwint, A.E.; Hartwell, J.K.; Heber, E.M.; Trivillin, V.; Castillo, J.; Wentzeis, L.; Sloan, P.; Wemple, C.A.

    2004-10-04

    Initial physical dosimetry measurements have been completed using activation spectrometry and thermoluminiscent dosimeters to characterize the BNCT irradiation facility developed at the RA-1 research reactor operated by the Argentine National Atomic Energy Commission in Buenos Aires. Some biological scoping irradiations have also been completed using a small-animal (hamster) oral mucosa tumor model. Results indicate that the RA-1 neutron source produces useful dose rates but that some improvements in the initial configuration will be needed to optimize the spectrum for thermal-neutron BNCT research applications.

  1. Biological Networks Entropies: Examples in Neural Memory Networks, Genetic Regulation Networks and Social Epidemic Networks

    Directory of Open Access Journals (Sweden)

    Jacques Demongeot

    2018-01-01

    Full Text Available Networks used in biological applications at different scales (molecule, cell and population are of different types: neuronal, genetic, and social, but they share the same dynamical concepts, in their continuous differential versions (e.g., non-linear Wilson-Cowan system as well as in their discrete Boolean versions (e.g., non-linear Hopfield system; in both cases, the notion of interaction graph G(J associated to its Jacobian matrix J, and also the concepts of frustrated nodes, positive or negative circuits of G(J, kinetic energy, entropy, attractors, structural stability, etc., are relevant and useful for studying the dynamics and the robustness of these systems. We will give some general results available for both continuous and discrete biological networks, and then study some specific applications of three new notions of entropy: (i attractor entropy, (ii isochronal entropy and (iii entropy centrality; in three domains: a neural network involved in the memory evocation, a genetic network responsible of the iron control and a social network accounting for the obesity spread in high school environment.

  2. Reconstruction of biological networks based on life science data integration

    Directory of Open Access Journals (Sweden)

    Kormeier Benjamin

    2010-06-01

    Full Text Available For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH - an integration toolkit for building life science data warehouses, CardioVINEdb - a information system for biological data in cardiovascular-disease and VANESA- a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

  3. Reconstruction of biological networks based on life science data integration.

    Science.gov (United States)

    Kormeier, Benjamin; Hippe, Klaus; Arrigo, Patrizio; Töpel, Thoralf; Janowski, Sebastian; Hofestädt, Ralf

    2010-10-27

    For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH--an integration toolkit for building life science data warehouses, CardioVINEdb--a information system for biological data in cardiovascular-disease and VANESA--a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

  4. Organization of excitable dynamics in hierarchical biological networks.

    Directory of Open Access Journals (Sweden)

    Mark Müller-Linow

    Full Text Available This study investigates the contributions of network topology features to the dynamic behavior of hierarchically organized excitable networks. Representatives of different types of hierarchical networks as well as two biological neural networks are explored with a three-state model of node activation for systematically varying levels of random background network stimulation. The results demonstrate that two principal topological aspects of hierarchical networks, node centrality and network modularity, correlate with the network activity patterns at different levels of spontaneous network activation. The approach also shows that the dynamic behavior of the cerebral cortical systems network in the cat is dominated by the network's modular organization, while the activation behavior of the cellular neuronal network of Caenorhabditis elegans is strongly influenced by hub nodes. These findings indicate the interaction of multiple topological features and dynamic states in the function of complex biological networks.

  5. Dosimetry; La dosimetrie

    Energy Technology Data Exchange (ETDEWEB)

    Le Couteulx, I.; Apretna, D.; Beaugerie, M.F. [Electricite de France (EDF), 75 - Paris (France)] [and others

    2003-07-01

    Eight articles treat the dosimetry. Two articles evaluate the radiation doses in specific cases, dosimetry of patients in radiodiagnosis, three articles are devoted to detectors (neutrons and x and gamma radiations) and a computer code to build up the dosimetry of an accident due to an external exposure. (N.C.)

  6. Design of a computation tool for neutron spectrometry and dosimetry through evolutionary neural networks

    International Nuclear Information System (INIS)

    Ortiz R, J. M.; Vega C, H. R.; Martinez B, M. R.; Gallego, E.

    2009-10-01

    The neutron dosimetry is one of the most complicated tasks of radiation protection, due to it is a complex technique and highly dependent of neutron energy. One of the first devices used to perform neutron spectrometry is the system known as spectrometric system of Bonner spheres, that continuous being one of spectrometers most commonly used. This system has disadvantages such as: the components weight, the low resolution of spectrum, long and drawn out procedure for the spectra reconstruction, which require an expert user in system management, the need of use a reconstruction code as BUNKIE, SAND, etc., which are based on an iterative reconstruction algorithm and whose greatest inconvenience is that for the spectrum reconstruction, are needed to provide to system and initial spectrum as close as possible to the desired spectrum get. Consequently, researchers have mentioned the need to developed alternative measurement techniques to improve existing monitoring systems for workers. Among these alternative techniques have been reported several reconstruction procedures based on artificial intelligence techniques such as genetic algorithms, artificial neural networks and hybrid systems of evolutionary artificial neural networks using genetic algorithms. However, the use of these techniques in the nuclear science area is not free of problems, so it has been suggested that more research is conducted in such a way as to solve these disadvantages. Because they are emerging technologies, there are no tools for the results analysis, so in this paper we present first the design of a computation tool that allow to analyze the neutron spectra and equivalent doses, obtained through the hybrid technology of neural networks and genetic algorithms. This tool provides an user graphical environment, friendly, intuitive and easy of operate. The speed of program operation is high, executing the analysis in a few seconds, so it may storage and or print the obtained information for

  7. Biological Dosimetry of X-rays by micronuclei study; Dosimetria Biologica de rayos-X mediante el estudio de micronucleos

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, E.; Silva, A.; Navlet, J.

    1991-07-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes citokinetics blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree centigree has been produced. Experimental data is fitted to model Y=C+ {alpha}D+BD''2 where Y is the number of micronuclei per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 24 refs.

  8. Biological Dosimetry of X-rays by micronuclei study; Dosimetria Biologica de rayos-X mediante el estudio de micronucleos

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, E; Silva, A; Navlet, J

    1991-07-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes citokinetics blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree centigree has been produced. Experimental data is fitted to model Y=C+ {alpha}D+BD''2 where Y is the number of micronuclei per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 24 refs.

  9. Extension of the biological effective dose to the MIRD schema and possible implications in radionuclide therapy dosimetry

    International Nuclear Information System (INIS)

    Baechler, Sebastien; Hobbs, Robert F.; Prideaux, Andrew R.; Wahl, Richard L.; Sgouros, George

    2008-01-01

    In dosimetry-based treatment planning protocols, patients with rapid clearance of the radiopharmaceutical require a larger amount of initial activity than those with slow clearance to match the absorbed dose to the critical organ. As a result, the dose-rate to the critical organ is higher in patients with rapid clearance and may cause unexpected toxicity compared to patients with slow clearance. In order to account for the biological impact of different dose-rates, radiobiological modeling is beginning to be applied to the analysis of radionuclide therapy patient data. To date, the formalism used for these analyses is based on kinetics derived from activity in a single organ, the target. This does not include the influence of other source organs to the dose and dose-rate to the target organ. As a result, only self-dose irradiation in the target organ contributes to the dose-rate. In this work, the biological effective dose (BED) formalism has been extended to include the effect of multiple source organ contributions to the net dose-rate in a target organ. The generalized BED derivation has been based on the Medical Internal Radionuclide Dose Committee (MIRD) schema assuming multiple source organs following exponential effective clearance of the radionuclide. A BED-based approach to determine the largest safe dose to critical organs has also been developed. The extended BED formalism is applied to red marrow dosimetry, as well as kidney dosimetry considering the cortex and the medulla separately, since both those organs are commonly dose limiting in radionuclide therapy. The analysis shows that because the red marrow is an early responding tissue (high α/β), it is less susceptible to unexpected toxicity arising from rapid clearance of high levels of administered activity in the marrow or in the remainder of the body. In kidney dosimetry, the study demonstrates a complex interplay between clearance of activity in the cortex and the medulla, as well as the initial

  10. Biological dosimetry of heavy ion induced chromosome lesions in human peripheral blood lymphocytes of different healthy donors

    International Nuclear Information System (INIS)

    Groesser, T.; Rydberg, B.; Ritter, S.; Hessel, P.; Kraft, G.

    2003-01-01

    Full text: In the presented work the effect of sparsely ionizing X-rays or densely ionizing carbon ions on human peripheral blood lymphocytes (PBL) from healthy donors regarding the fluctuations in radiosensitivity within the same donor and between different donors was examined. This is not only of special interest for physicians and radiation biologists but also plays an important role in space flights because such fluctuations in the radiation response would reduce the accuracy of the biological dosimetry. In this context, biological changes in the aberration rate of metaphase cells as well as in cell proliferation and the mitotic index were measured. Since chromosome analyses are presently the most powerful biological method to quantify radiation exposure, the study focused on the measurements of chromosome aberrations in first-metaphase cells. The investigations showed that the aberration yield after 400 MeV/u carbon ion exposure (LET = 11 keV/micrometer) was higher than after X-irradiation. The aberration yield in first mitotic cells as well as the proportion of damaged cells was stable over the examined period up to 72h after exposure to X-rays or carbon ions. Furthermore, the results of the presented work revealed pronounced fluctuations in the measured parameters in the same donor as well as between different donors. If the dose effect curves of such parameters were used as calibration curves for radiation dose assessment these fluctuations will decrease their potential of use for dose estimation. This demonstrates that a general calibration curve for dose assessment might not be sufficiently precise and individual calibration curves might improve the accuracy of the biological dosimetry

  11. Integration of genomic information with biological networks using Cytoscape.

    Science.gov (United States)

    Bauer-Mehren, Anna

    2013-01-01

    Cytoscape is an open-source software for visualizing, analyzing, and modeling biological networks. This chapter explains how to use Cytoscape to analyze the functional effect of sequence variations in the context of biological networks such as protein-protein interaction networks and signaling pathways. The chapter is divided into five parts: (1) obtaining information about the functional effect of sequence variation in a Cytoscape readable format, (2) loading and displaying different types of biological networks in Cytoscape, (3) integrating the genomic information (SNPs and mutations) with the biological networks, and (4) analyzing the effect of the genomic perturbation onto the network structure using Cytoscape built-in functions. Finally, we briefly outline how the integrated data can help in building mathematical network models for analyzing the effect of the sequence variation onto the dynamics of the biological system. Each part is illustrated by step-by-step instructions on an example use case and visualized by many screenshots and figures.

  12. Biological (DB) and internal dosimetry (DI) in patients with differentiated thyroid carcinoma (CaDT) treated with iodine 131

    International Nuclear Information System (INIS)

    Fadel, Ana M.; Chebel, G.; Oneto, A.; Di Giorgio, Marina; Vallerga, Maria B.; Taja, Maria R.; Radl, A.; Rojo, Ana M.; Deluca, G.; Levi de Cabrejas, Mariana; Cabrejas, Raul C.

    2009-01-01

    The internal 131 I radiotherapy in patients with CaDT is used within the therapeutic scheme as a step post-thyroidectomy. The success of therapy is to achieve a lethal dose in the tumor tissue without exceeding the dose of tolerance in healthy tissues (doses greater than 2 Gy in bone marrow could lead to myelotoxicity). In this work, the treatment protocol applied incorporates assessment by biological (DB) and internal dosimetry (DI) for estimating doses to the whole body and bone marrow to administer a therapeutic personalized for each patient. The estimate biological dose is based in the quantification of chromosomal aberrations, which is referred to a dose-response curve. Objectives: 1) To estimate the absorbed dose to the whole body and bone marrow due to the administration of 131 I therapy in patients with CaDT, by applying three different cytogenetic tests: conventional cytogenetics, micronuclei (MN) and fluorescence in situ hybridization (FISH); 2) Assess the correlation of the results obtained by DB and DI for personalization of treatment. Materials and methods: We evaluated 24 patients with CaDiT by applying the cytogenetic tests mentioned and internal dosimetry (methodology Mird-Olinda). Internal dosimetry: We administered a tracer dose 74 to 111 MBq. Measurements were made of activity in whole body and blood. By adjusting the scheme was estimated MIRD dose in bone marrow and the maximum therapeutic activity to manage and secure. Through software Olinda was determined absorbed dose to the whole body for each patient. We considered patient-specific data (physical frame size, weight, hematocrit) to adjust the methodology in each particular case. It is assumed that the tracer activity administered has a kinetic in the body similar to the 131 I to be administered in therapeutic amounts. Biology Dosimetry : We performed for each patient taking 2 sequential venous blood samples to estimate the dose due to therapeutic activity in review: the first shows, pre

  13. Cytogenetic techniques for biological indications and dosimetry of of radiation damages in humans

    International Nuclear Information System (INIS)

    Hadjidekova, V.

    2003-01-01

    The cytogenetic methods present a proved way for bio-monitoring and bio-dosimetry for persons, submitted to ionising radiation in occupational and emergency conditions. Their application complement and assist the evaluation of the physical dosimetry and takes in account the individual radiosensitivity of the organism. A comparative assessment is made of the cytogenetic markers for radiation damage of humans applied in Bulgaria. It is discussed the sensitivity of the methods and their development in the last years, as well as the basic concept for their application - the causal relationship between the frequency of the observation of cytogenetic markers in peripheral blood lymphocytes and the risk of oncological disease. The conventional analysis of dicentrics is recognised as a 'golden standard' for the quantitative assessment of the radiation damage. The long term persisting translocations reflect properly the cumulative dose burden from chronic exposure. The micronucleus test allows a quick screening of large groups of persons, working in ionising radiation environment. The combined application with centromeric DNA probe improves the sensitivity and presents a modern alternative of the bio-monitoring and bio-dosimetry. It is discussed the advantages of the different cytogenetic techniques and their optimised application for the assessment of the radiation impact on humans

  14. Reconstruction of absorbed dose by methods biological dosimetry inhabitans living in Semipalatinsk Nuclear Test Site

    International Nuclear Information System (INIS)

    Abildinova, G.

    2010-01-01

    As a result perennial overland and atmospheric test the nucleus weapon on Semipalatinsk nucler test site (NTS) about 1,2 ml person were subjected to frequentative sharp and chronic irradiation in different range of doses. Besides a significant number of battle radioactive matters tests with radionuclei dispersion on soil surface and an atmosphere was realized also. All this activity has caused the significant radioactive contamination and damage to an environment, and the local population has received extra exposure to radiation. These circumstances have essentially complicated the economy development of the given region. Aim: Reconstruction of absorbed dose by modern methods biological dosimetry beside inhabitants living in region of influence Semipalatinsk NTS. The cytogenetically examination of population Semipalatinsk region, living in different zones radiation risk: s. Dolon, s. Sarzhal, s. Mostik. Installed that total frequency of chromosome aberrations forms 4,8/100; 2,1/100; 2,5/100 cells, accordingly. High level of chromosome aberrations is conditioned to account radiations markers - acentric fragments (2,1/100 cells in s. Dolon; 1,09/100 cells in s. Sarzhal; 0,79/100 cells in s. Mostik); dysenteric and ring chromosomes (0,6; 0,2; 0,11) and stable type chromosome aberrations (1,02; 0,3; 1,0, accordingly). Frequency and spectrum of chromosome aberrations are indicative of significant mutation action ionizing radiations on chromosome device of somatic cells. Studied dependency an cytogenetically of effects from dose of irradiation within before 0,5 Gr in vitro for calibrated curve standard when undertaking reconstruction efficient dose at the time of irradiations examined group of population. Dependency is described the model a*cos(x) 1 + sin (x), where x - correlation a dysenteric and ring chromosomes to acentric fragments. Dependence of cytogenetic parameters upon ESR-doses had been studied. Had been received dependences: for the total frequency of

  15. Application of random matrix theory to biological networks

    Energy Technology Data Exchange (ETDEWEB)

    Luo Feng [Department of Computer Science, Clemson University, 100 McAdams Hall, Clemson, SC 29634 (United States); Department of Pathology, U.T. Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390-9072 (United States); Zhong Jianxin [Department of Physics, Xiangtan University, Hunan 411105 (China) and Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States)]. E-mail: zhongjn@ornl.gov; Yang Yunfeng [Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States); Scheuermann, Richard H. [Department of Pathology, U.T. Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390-9072 (United States); Zhou Jizhong [Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019 (United States) and Oak Ridge National Laboratory, Oak Ridge, TN 37831 (United States)]. E-mail: zhouj@ornl.gov

    2006-09-25

    We show that spectral fluctuation of interaction matrices of a yeast protein-protein interaction network and a yeast metabolic network follows the description of the Gaussian orthogonal ensemble (GOE) of random matrix theory (RMT). Furthermore, we demonstrate that while the global biological networks evaluated belong to GOE, removal of interactions between constituents transitions the networks to systems of isolated modules described by the Poisson distribution. Our results indicate that although biological networks are very different from other complex systems at the molecular level, they display the same statistical properties at network scale. The transition point provides a new objective approach for the identification of functional modules.

  16. Biological effects of radiation and dosimetry in X-ray diagnostics of children

    International Nuclear Information System (INIS)

    Milkovic, Durdica; Beck, Natko; Kovac, Kornelija; Garaj-Vrhovac, Vera; Gajski, Goran

    2008-01-01

    The chest radiograms represent the basic radiological examinations of thorax. The basis for radiation protection especially in pediatrics is the exact determination of doses. The risk estimation of genome damages can be received in human peripheral blood lymphocytes using alkaline version of Comet Assay. The aim of this work was assessment and quantification of the level of DNA damage in peripheral blood lymphocytes of children during airways X-ray examinations of chest and to compare data to the dose of exposure. Doses were determined using thermoluminescence (TL) dosimetry and radiophotoluminescent (RPL) glass dosimetry system. Twenty children with pulmonary diseases, ages between 5 and 14 years were assessed. Dose measurements were conducted for poster-anterior (PA) projection on the forehead, thyroid gland, gonads, chest and back. We used a 150 kV Shimadzu CH-200 M X-ray unit. Peripheral blood samples were taken from children after and prior to X-ray exposure and were examined with the alkaline Comet Assay. Comet Assay is one of the standard techniques for assessing genome damage with variety applications in genotoxicity testing as well as fundamental research in DNA damage and repair. As a measure of DNA damage tail length was used, calculated from the centre of the head and presented in micrometers (μm). Mean value of group after irradiation was 14.04 ± 1.74 as opposed to mean value of group before irradiation that was 13.15 ± 1.33. Differences between mean tail lengths were statistically significant (P<0.05, ANOVA). In addition, correlation was found between doses in primary beam (measured on the back) and the ratio of tail length (DNA damage) before and after irradiation. Doses measured with TL and RPL dosimeters showed satisfactory agreement and both dosimetry methods are suitable for dosimetric measurements in X-ray diagnostics. (author)

  17. OWL Reasoning Framework over Big Biological Knowledge Network

    Science.gov (United States)

    Chen, Huajun; Chen, Xi; Gu, Peiqin; Wu, Zhaohui; Yu, Tong

    2014-01-01

    Recently, huge amounts of data are generated in the domain of biology. Embedded with domain knowledge from different disciplines, the isolated biological resources are implicitly connected. Thus it has shaped a big network of versatile biological knowledge. Faced with such massive, disparate, and interlinked biological data, providing an efficient way to model, integrate, and analyze the big biological network becomes a challenge. In this paper, we present a general OWL (web ontology language) reasoning framework to study the implicit relationships among biological entities. A comprehensive biological ontology across traditional Chinese medicine (TCM) and western medicine (WM) is used to create a conceptual model for the biological network. Then corresponding biological data is integrated into a biological knowledge network as the data model. Based on the conceptual model and data model, a scalable OWL reasoning method is utilized to infer the potential associations between biological entities from the biological network. In our experiment, we focus on the association discovery between TCM and WM. The derived associations are quite useful for biologists to promote the development of novel drugs and TCM modernization. The experimental results show that the system achieves high efficiency, accuracy, scalability, and effectivity. PMID:24877076

  18. Biology Question Generation from a Semantic Network

    Science.gov (United States)

    Zhang, Lishan

    Science instructors need questions for use in exams, homework assignments, class discussions, reviews, and other instructional activities. Textbooks never have enough questions, so instructors must find them from other sources or generate their own questions. In order to supply instructors with biology questions, a semantic network approach was developed for generating open response biology questions. The generated questions were compared to professional authorized questions. To boost students' learning experience, adaptive selection was built on the generated questions. Bayesian Knowledge Tracing was used as embedded assessment of the student's current competence so that a suitable question could be selected based on the student's previous performance. A between-subjects experiment with 42 participants was performed, where half of the participants studied with adaptive selected questions and the rest studied with mal-adaptive order of questions. Both groups significantly improved their test scores, and the participants in adaptive group registered larger learning gains than participants in the control group. To explore the possibility of generating rich instructional feedback for machine-generated questions, a question-paragraph mapping task was identified. Given a set of questions and a list of paragraphs for a textbook, the goal of the task was to map the related paragraphs to each question. An algorithm was developed whose performance was comparable to human annotators. A multiple-choice question with high quality distractors (incorrect answers) can be pedagogically valuable as well as being much easier to grade than open-response questions. Thus, an algorithm was developed to generate good distractors for multiple-choice questions. The machine-generated multiple-choice questions were compared to human-generated questions in terms of three measures: question difficulty, question discrimination and distractor usefulness. By recruiting 200 participants from

  19. 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...

  20. 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

  1. Use of unstable chromosome aberrations for biological dosimetry after the first postirradiation mitosis

    International Nuclear Information System (INIS)

    Doloy, M.T.; Malarbet, J.L.; Guedeney, G.; Bourguignon, M.; Leroy, A.; Reillaudou, M.; Masse, R.

    1991-01-01

    The loss of unstable chromosome aberrations after the first postirradiation mitosis makes their use difficult in radiation dosimetry. We describe here a method which, in a cell population observed at this stage, allows retrospective estimation of the frequencies of the unstable aberrations induced at the time of irradiation, and their use as a dosimeter. The laws controlling the behavior of unstable aberrations during mitosis were defined from a large-scale experiment on irradiated human lymphocytes. For cells undergoing the first, second, or third mitosis after irradiation, relationships were determined between the frequency, at irradiation time, of acentric fragments not arising from formation of dicentrics or rings, and the ratio of dicentrics and centric rings appearing without acentric fragments to the total number of dicentrics plus rings. On the basis of this ratio, the method described here provides an assessment of the postirradiation mitotic activity in a cell population. This assessment permitted estimation of the cell distribution and frequency of dicentrics plus centric rings, and of the frequency of acentric fragments at the time of irradiation. The use of this method for retrospective dosimetry after whole-body irradiation under various conditions of exposure is illustrated

  2. A generic algorithm for layout of biological networks.

    Science.gov (United States)

    Schreiber, Falk; Dwyer, Tim; Marriott, Kim; Wybrow, Michael

    2009-11-12

    Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration. We present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks. The presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.

  3. The IAEA/WHO Network of SSDLs. Short history, activity and future trends[Secondary Standard Dosimetry Laboratories

    Energy Technology Data Exchange (ETDEWEB)

    Svensson, Hans; Zsdanszky, Kalman [International Atomic Energy Agency, Dosimtery Section, Vienna (Austria)

    1990-04-01

    In 1968 at an IAEA meeting in Caracas, Venezuela, the dosimetric requirements of radiotherapy centres were discussed. At that time many radiotherapy departments in developing countries did not have a dosimeter. Even those that had a dosimeter were seldom able to send it to a Primary Standard Dosimetry Laboratory (PSDL) for proper calibration. The establishment of regional dosimeter calibration laboratories was recommended by the participating experts including representatives of WHO. There was general consent that it was not necessary to establish in every country a PSDL, which would need a very qualified staff and sophisticated equipment. Instead, the establishment of Secondary Standard Dosimetry Laboratories (SSDLs) was found to be an adequate solution to the problem. The new idea of SSDLs and their role within the international metrology system was thoroughly discussed at a joint IAEA/WHO meeting in Rio de Janeiro (scientific secretaries: H.H. Eisenlohr, IAEA and W. Seelentag, WHO) in December 1974. Considering the fact that an SSDL cannot work in isolation the experts recommended the setting up of an international Network of SSDLs under the auspices of the IAEA and WHO. The statutes of the IAEA/WHO Network of SSDLs were laid down in a Working Arrangement between the IAEA and WHO in April 1976. Later in 1976 the two Directors General of the IAEA and WHO formally announced by circular letters to their respective member states the establishment of the IAEA/WHO Network of SSDL. The Criteria for the Establishment of a Secondary Standard Dosimetry Laboratory were formulated by an Advisory Group and were attached to these letters. At that time there existed already 8 laboratories, which had been designated by WHO during the period 1968-1976 as regional reference centres for dosimetry. Another SSDL had been set up in Rio de Janeiro in collaboration between the Brazilian Government, the Government of the Federal Republic of Germany, and the IAEA. As a consequence of the

  4. BioNSi: A Discrete Biological Network Simulator Tool.

    Science.gov (United States)

    Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

    2016-08-05

    Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found.

  5. Internal sources dosimetry

    International Nuclear Information System (INIS)

    Savio, Eduardo

    1994-01-01

    The absorbed dose, need of estimation in risk evaluation in the application of radiopharmaceuticals in Nuclear Medicine practice,internal dosimetry,internal and external sources. Calculation methodology,Marinelli model,MIRD system for absorbed dose calculation based on biological parameters of radiopharmaceutical in human body or individual,energy of emitted radiations by administered radionuclide, fraction of emitted energy that is absorbed by target body.Limitation of the MIRD calculation model. A explanation of Marinelli method of dosimetry calculation,β dosimetry. Y dosimetry, effective dose, calculation in organs and tissues, examples. Bibliography .

  6. Power Laws, Scale-Free Networks and Genome Biology

    CERN Document Server

    Koonin, Eugene V; Karev, Georgy P

    2006-01-01

    Power Laws, Scale-free Networks and Genome Biology deals with crucial aspects of the theoretical foundations of systems biology, namely power law distributions and scale-free networks which have emerged as the hallmarks of biological organization in the post-genomic era. The chapters in the book not only describe the interesting mathematical properties of biological networks but moves beyond phenomenology, toward models of evolution capable of explaining the emergence of these features. The collection of chapters, contributed by both physicists and biologists, strives to address the problems in this field in a rigorous but not excessively mathematical manner and to represent different viewpoints, which is crucial in this emerging discipline. Each chapter includes, in addition to technical descriptions of properties of biological networks and evolutionary models, a more general and accessible introduction to the respective problems. Most chapters emphasize the potential of theoretical systems biology for disco...

  7. Activating and inhibiting connections in biological network dynamics

    Directory of Open Access Journals (Sweden)

    Knight Rob

    2008-12-01

    Full Text Available Abstract Background Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior – for example, whether deleting a protein from a signaling network would maintain the network's dynamical behavior, or induce oscillations or chaos. Results Here we report that the balance between activating and inhibiting connections is important in determining whether network dynamics reach steady state or oscillate. We use a simple dynamical model of a network of interacting genes or proteins. Using the model, we study random networks, networks selected for robust dynamics, and examples of biological network topologies. The fraction of activating connections influences whether the network dynamics reach steady state or oscillate. Conclusion The activating fraction may predispose a network to oscillate or reach steady state, and neutral evolution or selection of this parameter may affect the behavior of biological networks. This principle may unify the dynamics of a wide range of cellular networks. Reviewers Reviewed by Sergei Maslov, Eugene Koonin, and Yu (Brandon Xia (nominated by Mark Gerstein. For the full reviews, please go to the Reviewers' comments section.

  8. Mining biological networks from full-text articles.

    Science.gov (United States)

    Czarnecki, Jan; Shepherd, Adrian J

    2014-01-01

    The study of biological networks is playing an increasingly important role in the life sciences. Many different kinds of biological system can be modelled as networks; perhaps the most important examples are protein-protein interaction (PPI) networks, metabolic pathways, gene regulatory networks, and signalling networks. Although much useful information is easily accessible in publicly databases, a lot of extra relevant data lies scattered in numerous published papers. Hence there is a pressing need for automated text-mining methods capable of extracting such information from full-text articles. Here we present practical guidelines for constructing a text-mining pipeline from existing code and software components capable of extracting PPI networks from full-text articles. This approach can be adapted to tackle other types of biological network.

  9. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

    Science.gov (United States)

    Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

    2015-01-01

    With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

  10. Node fingerprinting: an efficient heuristic for aligning biological networks.

    Science.gov (United States)

    Radu, Alex; Charleston, Michael

    2014-10-01

    With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

  11. On the Interplay between the Evolvability and Network Robustness in an Evolutionary Biological Network: A Systems Biology Approach

    Science.gov (United States)

    Chen, Bor-Sen; Lin, Ying-Po

    2011-01-01

    In the evolutionary process, the random transmission and mutation of genes provide biological diversities for natural selection. In order to preserve functional phenotypes between generations, gene networks need to evolve robustly under the influence of random perturbations. Therefore, the robustness of the phenotype, in the evolutionary process, exerts a selection force on gene networks to keep network functions. However, gene networks need to adjust, by variations in genetic content, to generate phenotypes for new challenges in the network’s evolution, ie, the evolvability. Hence, there should be some interplay between the evolvability and network robustness in evolutionary gene networks. In this study, the interplay between the evolvability and network robustness of a gene network and a biochemical network is discussed from a nonlinear stochastic system point of view. It was found that if the genetic robustness plus environmental robustness is less than the network robustness, the phenotype of the biological network is robust in evolution. The tradeoff between the genetic robustness and environmental robustness in evolution is discussed from the stochastic stability robustness and sensitivity of the nonlinear stochastic biological network, which may be relevant to the statistical tradeoff between bias and variance, the so-called bias/variance dilemma. Further, the tradeoff could be considered as an antagonistic pleiotropic action of a gene network and discussed from the systems biology perspective. PMID:22084563

  12. Applications, dosimetry and biological interactions of static and time-varying magnetic fields

    International Nuclear Information System (INIS)

    Tenforde, T.S.

    1988-08-01

    The primary topics of this presentation include: (1) the applications of magnetic fields in research, industry, and medical technologies; (2) mechanisms of interaction of static and time-varying magnetic fields with living systems; (3) human health effects of exposure to static and time-varying magnetic fields in occupational, medical, and residential settings; and (4) recent advances in the dosimetry of extremely-low-frequency electromagnetic fields. The discussion of these topics is centered about two issues of considerable contemporary interest: (1) potential health effects of the fields used in magnetic resonance imaging and in vivo spectroscopy, and (2) the controversial issue of whether exposure to extremely-low-frequency (ELF) electromagnetic fields in the home and workplace leads to an elevated risk of cancer. 11 refs

  13. Communication on the structure of biological networks

    Indian Academy of Sciences (India)

    Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from different domains may vary quite significantly. As there is an interplay between network architecture and dynamics, structure plays an important role in communication and spreading of ...

  14. Advances in biomedical dosimetry

    International Nuclear Information System (INIS)

    1981-01-01

    Full text: Radiation dosimetry, the accurate determination of the absorbed dose within an irradiated body or a piece of material, is a prerequisite for all applications of ionizing radiation. This has been known since the very first radiation applications in medicine and biology, and increasing efforts are being made by radiation researchers to develop more reliable, effective and safe instruments, and to further improve dosimetric accuracy for all types of radiation used. Development of new techniques and instrumentation was particularly fast in the field of both medical diagnostic and therapeutic radiology. Thus, in Paris in October the IAEA held the latest symposium in its continuing series on dosimetry in medicine and biology. The last one was held in Vienna in 1975. High-quality dosimetry is obviously of great importance for human health, whether the objectives lie in the prevention and control of risks associated with the nuclear industry, in medical uses of radioactive substances or X-ray beams for diagnostic purposes, or in the application of photon, electron or neutron beams in radiotherapy. The symposium dealt with the following subjects: General aspects of dosimetry; Special physical and biomedical aspects; Determination of absorbed dose; Standardization and calibration of dosimetric systems; and Development of dosimetric systems. The forty or so papers presented and the discussions that followed them brought out a certain number of dominant themes, among which three deserve particular mention. - The recent generalization of the International System of Units having prompted a fundamental reassessment of the dosimetric quantities to be considered in calibrating measuring instruments, various proposals were advanced by the representatives of national metrology laboratories to replace the quantity 'exposure' (SI unit = coulomb/kg) by 'Kerma' or 'absorbed dose' (unit joule/kg, the special name of which is 'gray'), this latter being closer to the practical

  15. The effect of network biology on drug toxicology

    DEFF Research Database (Denmark)

    Gautier, Laurent; Taboureau, Olivier; Audouze, Karine Marie Laure

    2013-01-01

    Introduction: The high failure rate of drug candidates due to toxicity, during clinical trials, is a critical issue in drug discovery. Network biology has become a promising approach, in this regard, using the increasingly large amount of biological and chemical data available and combining...... it with bioinformatics. With this approach, the assessment of chemical safety can be done across multiple scales of complexity from molecular to cellular and system levels in human health. Network biology can be used at several levels of complexity. Areas covered: This review describes the strengths and limitations...... of network biology. The authors specifically assess this approach across different biological scales when it is applied to toxicity. Expert opinion: There has been much progress made with the amount of data that is generated by various omics technologies. With this large amount of useful data, network...

  16. Local and global control of ecological and biological networks

    OpenAIRE

    Alessandro Ferrarini

    2014-01-01

    Recently, I introduced a methodological framework so that ecological and biological networks can be controlled both from inside and outside by coupling network dynamics and evolutionary modelling. The endogenous control requires the network to be optimized at the beginning of its dynamics (by acting upon nodes, edges or both) so that it will then go inertially to the desired state. Instead, the exogenous control requires that exogenous controllers act upon the network at each time step. By th...

  17. Identification of important nodes in directed biological networks: a network motif approach.

    Directory of Open Access Journals (Sweden)

    Pei Wang

    Full Text Available Identification of important nodes in complex networks has attracted an increasing attention over the last decade. Various measures have been proposed to characterize the importance of nodes in complex networks, such as the degree, betweenness and PageRank. Different measures consider different aspects of complex networks. Although there are numerous results reported on undirected complex networks, few results have been reported on directed biological networks. Based on network motifs and principal component analysis (PCA, this paper aims at introducing a new measure to characterize node importance in directed biological networks. Investigations on five real-world biological networks indicate that the proposed method can robustly identify actually important nodes in different networks, such as finding command interneurons, global regulators and non-hub but evolutionary conserved actually important nodes in biological networks. Receiver Operating Characteristic (ROC curves for the five networks indicate remarkable prediction accuracy of the proposed measure. The proposed index provides an alternative complex network metric. Potential implications of the related investigations include identifying network control and regulation targets, biological networks modeling and analysis, as well as networked medicine.

  18. MIRD Commentary: Proposed Name for a Dosimetry Unit Applicable to Deterministic Biological Effects-The Barendsen (Bd)

    International Nuclear Information System (INIS)

    Sgouros, George; Howell, R. W.; Bolch, Wesley E.; Fisher, Darrell R.

    2009-01-01

    The fundamental physical quantity for relating all biologic effects to radiation exposure is the absorbed dose, the energy imparted per unit mass of tissue. Absorbed dose is expressed in units of joules per kilogram (J/kg) and is given the special name gray (Gy). Exposure to ionizing radiation may cause both deterministic and stochastic biologic effects. To account for the relative effect per unit absorbed dose that has been observed for different types of radiation, the International Commission on Radiological Protection (ICRP) has established radiation weighting factors for stochastic effects. The product of absorbed dose in Gy and the radiation weighting factor is defined as the equivalent dose. Equivalent dose values are designated by a special named unit, the sievert (Sv). Unlike the situation for stochastic effects, no well-defined formalism and associated special named quantities have been widely adopted for deterministic effects. The therapeutic application of radionuclides and, specifically, -particle emitters in nuclear medicine has brought to the forefront the need for a well-defined dosimetry formalism applicable to deterministic effects that is accompanied by corresponding special named quantities. This commentary reviews recent proposals related to this issue and concludes with a recommendation to establish a new named quantity

  19. SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

    Science.gov (United States)

    Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J

    2013-01-01

    We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases.

  20. Controllability and observability of Boolean networks arising from biology

    Science.gov (United States)

    Li, Rui; Yang, Meng; Chu, Tianguang

    2015-02-01

    Boolean networks are currently receiving considerable attention as a computational scheme for system level analysis and modeling of biological systems. Studying control-related problems in Boolean networks may reveal new insights into the intrinsic control in complex biological systems and enable us to develop strategies for manipulating biological systems using exogenous inputs. This paper considers controllability and observability of Boolean biological networks. We propose a new approach, which draws from the rich theory of symbolic computation, to solve the problems. Consequently, simple necessary and sufficient conditions for reachability, controllability, and observability are obtained, and algorithmic tests for controllability and observability which are based on the Gröbner basis method are presented. As practical applications, we apply the proposed approach to several different biological systems, namely, the mammalian cell-cycle network, the T-cell activation network, the large granular lymphocyte survival signaling network, and the Drosophila segment polarity network, gaining novel insights into the control and/or monitoring of the specific biological systems.

  1. Dosimetry of internal emitters

    International Nuclear Information System (INIS)

    Anon.

    1982-01-01

    The Dosimetry of Internal Emitter Program endeavors to refine the correlation between radiation dose and observed biological effects. The program is presently engaged in the development of studies that will demonstrate the applicability of microdosimetry models developed under the Microdosimetry of Internal Sources Program. The program also provides guidance and assistance to Pacific Northwest Laboratory's Biology Department in the dosimetric analysis of internally deposited radionuclides. This report deals with alpha particle dosimetry plutonium 239 inhalation, and in vitro studies of chromosomal observations

  2. Contribution of new cytogenetic techniques in the estimations of old irradiations in retrospective biological dosimetry

    International Nuclear Information System (INIS)

    Pouzoulet, F.

    2007-10-01

    The objective of this study was to answer three questions: if the translocations are steady: the results have shown that the translocations even if they are not obligatory steady can be used in retrospective dosimetry. Furthermore, it appeared important to consider the complex translocations in view of their relative stability and complementary information they bring ( quality of radiation, received dose). The second question is what contribution of the M-F.I.S.H. in the translocations analysis in comparison with the F.I.S.H.-3: we have shown that the M-F.I.S.H. would allow to raise the whole of doubt due to a partial genome observation. that has for effect to increase the precision of the analysis and that what ever be the received dose. The third question is if there are differences between the chromosomal aberrations generated by x radiation of 50 keV and by gamma radiation from cobalt-60: yes, the low energy photons generate more translocations than the photons coming from cobalt-60. But they generate less dicentrics. this difference comes from the way the energy is deposited that leads to a more important formation of complex and multiple translocations with the low energy photons. this could constitute a problem in the use of low energy photons in radiotherapy. it would seem that the simple translocations rate is not influenced by the photons energy. (N.C.)

  3. Systems biology: properties of reconstructed networks

    National Research Council Canada - National Science Library

    Palsson, Bernhard

    2006-01-01

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

  4. The Structure and Function of Biological Networks

    Science.gov (United States)

    Wu, Daniel Duanqing

    2010-01-01

    Biology has been revolutionized in recent years by an explosion in the availability of data. Transforming this new wealth of data into meaningful biological insights and clinical breakthroughs requires a complete overhaul both in the questions being asked and the methodologies used to answer them. A major challenge in organizing and understanding…

  5. Neutron spectrometry and dosimetry with neural networks and Bonner spheres: a study to reduce the spheres number

    International Nuclear Information System (INIS)

    Espinoza G, J. G.; Martinez B, M. R.; Leon P, A. A.; Hernandez P, C. F.; Castaneda M, V. H.; Solis S, L. O.; Castaneda M, R.; Ortiz R, J. M.; Vega C, H. R.; Mendez, R.; Gallego, E.; De Sousa L, M. A.

    2016-10-01

    For neutron spectrometry and neutron dosimetry, the Bonner spheres spectrometric system has been the most widely used system, however, the number, size and weight of the spheres composing the system, as well as the need to use a reconstruction code and the long periods of time used to carry out the measurements are some of the disadvantages of this system. For the reconstruction of the spectra, different techniques such as artificial neural networks of reverse propagation have been used. The objective of this work was to reduce the number of Bonner spheres and to use counting speeds in a reverse propagation neural network, optimized by means of the robust design methodology, to reconstruct the neutron spectra. For the design of the neural network we used the neutron spectra of the IAEA and the response matrix of the Bonner spheres with "6LiI(Eu) detector. The performance of the network was compared; using 7 Bonner spheres against other cases where only 2 and one sphere are used. The network topologies were trained 36 times for each case keeping constant the objective error (1E(-3)), the training algorithm was trains cg and the robust design methodology to determine the best network architectures. With these, the best and worst results were compared. The results obtained using 7 spheres were similar to those with the 5-in sphere, however is still in an information analysis stage. (Author)

  6. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

    Science.gov (United States)

    Papin, Jason A; Reed, Jennifer L; Palsson, Bernhard O

    2004-12-01

    As reconstructed biochemical reaction networks continue to grow in size and scope, there is a growing need to describe the functional modules within them. Such modules facilitate the study of biological processes by deconstructing complex biological networks into conceptually simple entities. The definition of network modules is often based on intuitive reasoning. As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration.

  7. Epigenetics and Why Biological Networks are More Controllable than Expected

    Science.gov (United States)

    Motter, Adilson

    2013-03-01

    A fundamental property of networks is that perturbations to one node can affect other nodes, potentially causing the entire system to change behavior or fail. In this talk, I will show that it is possible to exploit this same principle to control network behavior. This approach takes advantage of the nonlinear dynamics inherent to real networks, and allows bringing the system to a desired target state even when this state is not directly accessible or the linear counterpart is not controllable. Applications show that this framework permits both reprogramming a network to a desired task as well as rescuing networks from the brink of failure, which I will illustrate through various biological problems. I will also briefly review the progress our group has made over the past 5 years on related control of complex networks in non-biological domains.

  8. In-situ fluorescence hybridization applied to biological dosimetry: contribution of automation to the counting of radio-induced chromosome aberrations

    International Nuclear Information System (INIS)

    Germain Thomas Roy, Laurence

    1999-01-01

    The frequency of chromosome aberrations on peripheral blood lymphocytes is a dose indicator in the case of ionizing radiations over-exposure. Stable chromosome aberrations (translocations, insertions) are visualized after labelling of some chromosomes using the fluorescence in-situ hybridization (FISH). The study of the use of the FISH technique in biological dosimetry is done with dose-effect curves. It seems that a bias is introduced during the observation of chromosome aberrations involving only 3 pairs of chromosomes. In order to avoid this bias, it would be useful to test the feasibility of using the multi-FISH technique in biological dosimetry. Moreover, this type of chromosome aberration changes with the type of irradiation. It is thus important to define the aberrations to be considered when the FISH technique is used. In order to reduce the time of image analysis, the CYTOGEN system, developed by IMSTAR company (Paris, France) has been adapted to the needs of biological dosimetry. This system allows to localize automatically the metaphases on the slide, which reduces the observation time by 2 or 4. An automatic detection protocol for chromosome aberrations has been implemented. It comprises the image capture, the contours detection and the classification of some chromosome aberrations. The different steps of this protocol have been tested in order to check that no bias is introduced by the automation. However, because radio-induced aberrations are rare events, it seems that a totally automatic system is not foreseeable. A semi-automatic analysis is more suitable. The use of the Slit-Scan technology (Laboratory of applied physics, Heidelberg, Germany) in biological dosimetry has been studied too. This technique allows to analyze rapidly a huge number of chromosomes. A good correlation has been observed between the dicentric frequency measured automatically and by manual counting. The system is under development and should be adapted to the detection of

  9. Integration of new biological and physical retrospective dosimetry methods into EU emergency response plans - joint RENEB and EURADOS inter-laboratory comparisons.

    Science.gov (United States)

    Ainsbury, Elizabeth; Badie, Christophe; Barnard, Stephen; Manning, Grainne; Moquet, Jayne; Abend, Michael; Antunes, Ana Catarina; Barrios, Lleonard; Bassinet, Celine; Beinke, Christina; Bortolin, Emanuela; Bossin, Lily; Bricknell, Clare; Brzoska, Kamil; Buraczewska, Iwona; Castaño, Carlos Huertas; Čemusová, Zina; Christiansson, Maria; Cordero, Santiago Mateos; Cosler, Guillaume; Monaca, Sara Della; Desangles, François; Discher, Michael; Dominguez, Inmaculada; Doucha-Senf, Sven; Eakins, Jon; Fattibene, Paola; Filippi, Silvia; Frenzel, Monika; Georgieva, Dimka; Gregoire, Eric; Guogyte, Kamile; Hadjidekova, Valeria; Hadjiiska, Ljubomira; Hristova, Rositsa; Karakosta, Maria; Kis, Enikő; Kriehuber, Ralf; Lee, Jungil; Lloyd, David; Lumniczky, Katalin; Lyng, Fiona; Macaeva, Ellina; Majewski, Matthaeus; Vanda Martins, S; McKeever, Stephen W S; Meade, Aidan; Medipally, Dinesh; Meschini, Roberta; M'kacher, Radhia; Gil, Octávia Monteiro; Montero, Alegria; Moreno, Mercedes; Noditi, Mihaela; Oestreicher, Ursula; Oskamp, Dominik; Palitti, Fabrizio; Palma, Valentina; Pantelias, Gabriel; Pateux, Jerome; Patrono, Clarice; Pepe, Gaetano; Port, Matthias; Prieto, María Jesús; Quattrini, Maria Cristina; Quintens, Roel; Ricoul, Michelle; Roy, Laurence; Sabatier, Laure; Sebastià, Natividad; Sholom, Sergey; Sommer, Sylwester; Staynova, Albena; Strunz, Sonja; Terzoudi, Georgia; Testa, Antonella; Trompier, Francois; Valente, Marco; Hoey, Olivier Van; Veronese, Ivan; Wojcik, Andrzej; Woda, Clemens

    2017-01-01

    RENEB, 'Realising the European Network of Biodosimetry and Physical Retrospective Dosimetry,' is a network for research and emergency response mutual assistance in biodosimetry within the EU. Within this extremely active network, a number of new dosimetry methods have recently been proposed or developed. There is a requirement to test and/or validate these candidate techniques and inter-comparison exercises are a well-established method for such validation. The authors present details of inter-comparisons of four such new methods: dicentric chromosome analysis including telomere and centromere staining; the gene expression assay carried out in whole blood; Raman spectroscopy on blood lymphocytes, and detection of radiation-induced thermoluminescent signals in glass screens taken from mobile phones. In general the results show good agreement between the laboratories and methods within the expected levels of uncertainty, and thus demonstrate that there is a lot of potential for each of the candidate techniques. Further work is required before the new methods can be included within the suite of reliable dosimetry methods for use by RENEB partners and others in routine and emergency response scenarios.

  10. Activities of Project 'Cooperation and development with Latin America and Iberian in Biological Dosimetry of Iberian Group of Radiation Protection Societies

    International Nuclear Information System (INIS)

    Nasazzi, Nora B.; Taja, Maria R.; Giorgio, Marina di; Garcia Lima, Omar; Lamadrid, Ana I.; Olivares, Pilar; Moreno, Mercedes; Prieto, Maria J.; Espinosa, Marco

    2001-01-01

    In 1996 the GRIAPRA Group (Latin American and Iberian Group of Radiation Protection Societies) was established with the participation of Argentina, Brazil, Cuba, Mexico, Peru, Portugal and Spain. In 1998 began the biennial Collaborative Working Project 'Cooperation and Development with Latin America in Biological Dosimetry', partially supported by the Extremadura Government, Spain, initially involving five countries: Argentina, Cuba, Peru, Portugal and Spain. The general aim of the project is to create an Latin American and Iberian Biological Dosimetry Laboratories Coordinated Group in order to: give mutual cooperation and to other countries if required, in the case of radiological accident; contribute to enhance the technical capabilities of the participant laboratories; promote the installment of laboratories on this field in countries that does not have it yet through the training of human resources and providing the necessary equipment and, finally, perform jointly research activities in biological dosimetry. The activities designed in order to accomplish the project specific aims for the 1998-2000 period have been achieved. Description and results are presented. (author)

  11. Review of retrospective dosimetry techniques for external ionising radiation exposures

    International Nuclear Information System (INIS)

    Ainsbury, E. A.; Bakhanova, E.; Barquinero, J. F.; Brai, M.; Chumak, V.; Correcher, V.; Darroudi, F.; Fattibene, P.; Gruel, G.; Guclu, I.; Horn, S.; Jaworska, A.; Kulka, U.; Lindholm, C.; Lloyd, D.; Longo, A.; Marrale, M.; Monteiro Gil, O.; Oestreicher, U.; Pajic, J.; Rakic, B.; Romm, H.; Trompier, F.; Veronese, I.; Voisin, P.; Vral, A.; Whitehouse, C. A.; Wieser, A.; Woda, C.; Wojcik, A.; Rothkamm, K.

    2011-01-01

    The current focus on networking and mutual assistance in the management of radiation accidents or incidents has demonstrated the importance of a joined-up approach in physical and biological dosimetry. To this end, the European Radiation Dosimetry Working Group 10 on 'Retrospective Dosimetry' has been set up by individuals from a wide range of disciplines across Europe. Here, established and emerging dosimetry methods are reviewed, which can be used immediately and retrospectively following external ionising radiation exposure. Endpoints and assays include dicentrics, translocations, premature chromosome condensation, micronuclei, somatic mutations, gene expression, electron paramagnetic resonance, thermoluminescence, optically stimulated luminescence, neutron activation, haematology, protein biomarkers and analytical dose reconstruction. Individual characteristics of these techniques, their limitations and potential for further development are reviewed, and their usefulness in specific exposure scenarios is discussed. Whilst no single technique fulfils the criteria of an ideal dosemeter, an integrated approach using multiple techniques tailored to the exposure scenario can cover most requirements. (authors)

  12. The Utility of Lymphocyte Premature Chromosome Condensation Analysis for Biological Dosimetry Following Accidental Overexposure to Ionising Radiation

    International Nuclear Information System (INIS)

    Chambrette, V.; Laval, F.; Voisin, P.

    1999-01-01

    Premature chromosome condensation (PCC) appears to have a possible utility for biological dosimetry purposes. The PCC technique may be adapted for cases of suspicion of overexposure where sampling is performed at least one day after an accident. For this purpose, human blood samples were exposed in vitro to 60 Co (0.5 Gy.min -1 ) up to 4 Gy and the PCC technique was performed after 24 h, 48 h, and 72 h of DNA repair at 37 deg. C. Analysis of excess PCC fragments distribution showed an overdispersion and the dose-effect relationship was best characterised by linear regression. Radiation-induced damage was reduced to 32% between the first and the second day of repair and to 42% the following day. Statistical precision of the dose was found to be dependent on the irradiation dose and on the number of cells examined. The necessity to establish dose-response relationships after different periods of DNA repair is demonstrated, and the use of PCC excess fragments yield as a bioindicator should take this fact into account. (author)

  13. Two classes of bipartite networks: nested biological and social systems.

    Science.gov (United States)

    Burgos, Enrique; Ceva, Horacio; Hernández, Laura; Perazzo, R P J; Devoto, Mariano; Medan, Diego

    2008-10-01

    Bipartite graphs have received some attention in the study of social networks and of biological mutualistic systems. A generalization of a previous model is presented, that evolves the topology of the graph in order to optimally account for a given contact preference rule between the two guilds of the network. As a result, social and biological graphs are classified as belonging to two clearly different classes. Projected graphs, linking the agents of only one guild, are obtained from the original bipartite graph. The corresponding evolution of its statistical properties is also studied. An example of a biological mutualistic network is analyzed in detail, and it is found that the model provides a very good fitting of all the main statistical features. The model also provides a proper qualitative description of the same features observed in social webs, suggesting the possible reasons underlying the difference in the organization of these two kinds of bipartite networks.

  14. Arrangement between the International Atomic Energy Agency and the World Health Organization concerning the establishment and operation of a network of Secondary Standard Dosimetry Laboratories

    International Nuclear Information System (INIS)

    1986-01-01

    The International Atomic Energy Agency (IAEA) and the World Health Organization (WHO), recognizing that they have been co-operating in the operation of a network of Secondary Standard Dosimetry Laboratories (the Network), established pursuant to a Working Arrangement, dated 5 April 1976; and desiring to continue this co-operation in accordance with Article V of the relationship agreement concluded by IAEA and WHO in 1959; hereby enter a new arrangement to guide their work in operating the Network and providing assistance, when needed, to individual Secondary Standard Dosimetry Laboratories (SSDLs). The purpose of this Arrangement is to set forth responsibilities of IAEA and WHO in the operation and support of the Network and to establish criteria for SSDLs

  15. Networks in biological systems: An investigation of the Gene Ontology as an evolving network

    International Nuclear Information System (INIS)

    Coronnello, C; Tumminello, M; Micciche, S; Mantegna, R.N.

    2009-01-01

    Many biological systems can be described as networks where different elements interact, in order to perform biological processes. We introduce a network associated with the Gene Ontology. Specifically, we construct a correlation-based network where the vertices are the terms of the Gene Ontology and the link between each two terms is weighted on the basis of the number of genes that they have in common. We analyze a filtered network obtained from the correlation-based network and we characterize its evolution over different releases of the Gene Ontology.

  16. Synthesis, biological distribution and radiation dosimetry of Te-123m analogues of hexadecenoic acid

    International Nuclear Information System (INIS)

    Basmadjian, G.P.; Ice, R.D.; Mills, S.L.

    1982-01-01

    The synthesis and biological distribution of four Te-123m analogues of hexadecenoic acid in rats, rabbits and dogs were described for use as possible myocardial imaging agents. The heart-to-blood ratios ranged from 0.13 for 3-telluranonadecenoic acid in rats at 5 mins to 6.25 for 18-methyl-17-tellura-9-nonadecenoic acid in dogs at 24 hrs. The biological half-life of the Te-123m labelled fatty acids ranged from 26 to 583 hrs in the hearts of the test animals. These Te-123m fatty acids were retained in the heart longer than radioiodinated fatty acids and have acceptable absorbed doses to the various target organs. (U.K.)

  17. Biological impacts and context of network theory

    Energy Technology Data Exchange (ETDEWEB)

    Almaas, E

    2007-01-05

    Many complex systems can be represented and analyzed as networks, and examples that have benefited from this approach span the natural sciences. For instance, we now know that systems as disparate as the World-Wide Web, the Internet, scientific collaborations, food webs, protein interactions and metabolism all have common features in their organization, the most salient of which are their scale-free connectivity distributions and their small-world behavior. The recent availability of large scale datasets that span the proteome or metabolome of an organism have made it possible to elucidate some of the organizational principles and rules that govern their function, robustness and evolution. We expect that combining the currently separate layers of information from gene regulatory-, signal transduction-, protein interaction- and metabolic networks will dramatically enhance our understanding of cellular function and dynamics.

  18. OEDIPE, a software for personalized Monte Carlo dosimetry and treatment planning optimization in nuclear medicine: absorbed dose and biologically effective dose considerations

    International Nuclear Information System (INIS)

    Petitguillaume, A.; Broggio, D.; Franck, D.; Desbree, A.; Bernardini, M.; Labriolle Vaylet, C. de

    2014-01-01

    For targeted radionuclide therapies, treatment planning usually consists of the administration of standard activities without accounting for the patient-specific activity distribution, pharmacokinetics and dosimetry to organs at risk. The OEDIPE software is a user-friendly interface which has an automation level suitable for performing personalized Monte Carlo 3D dosimetry for diagnostic and therapeutic radionuclide administrations. Mean absorbed doses to regions of interest (ROIs), isodose curves superimposed on a personalized anatomical model of the patient and dose-volume histograms can be extracted from the absorbed dose 3D distribution. Moreover, to account for the differences in radiosensitivity between tumoral and healthy tissues, additional functionalities have been implemented to calculate the 3D distribution of the biologically effective dose (BED), mean BEDs to ROIs, isoBED curves and BED-volume histograms along with the Equivalent Uniform Biologically Effective Dose (EUD) to ROIs. Finally, optimization tools are available for treatment planning optimization using either the absorbed dose or BED distributions. These tools enable one to calculate the maximal injectable activity which meets tolerance criteria to organs at risk for a chosen fractionation protocol. This paper describes the functionalities available in the latest version of the OEDIPE software to perform personalized Monte Carlo dosimetry and treatment planning optimization in targeted radionuclide therapies. (authors)

  19. Using biological networks to improve our understanding of infectious diseases

    Directory of Open Access Journals (Sweden)

    Nicola J. Mulder

    2014-08-01

    Full Text Available Infectious diseases are the leading cause of death, particularly in developing countries. Although many drugs are available for treating the most common infectious diseases, in many cases the mechanism of action of these drugs or even their targets in the pathogen remain unknown. In addition, the key factors or processes in pathogens that facilitate infection and disease progression are often not well understood. Since proteins do not work in isolation, understanding biological systems requires a better understanding of the interconnectivity between proteins in different pathways and processes, which includes both physical and other functional interactions. Such biological networks can be generated within organisms or between organisms sharing a common environment using experimental data and computational predictions. Though different data sources provide different levels of accuracy, confidence in interactions can be measured using interaction scores. Connections between interacting proteins in biological networks can be represented as graphs and edges, and thus studied using existing algorithms and tools from graph theory. There are many different applications of biological networks, and here we discuss three such applications, specifically applied to the infectious disease tuberculosis, with its causative agent Mycobacterium tuberculosis and host, Homo sapiens. The applications include the use of the networks for function prediction, comparison of networks for evolutionary studies, and the generation and use of host–pathogen interaction networks.

  20. Applying differential dynamic logic to reconfigurable biological networks.

    Science.gov (United States)

    Figueiredo, Daniel; Martins, Manuel A; Chaves, Madalena

    2017-09-01

    Qualitative and quantitative modeling frameworks are widely used for analysis of biological regulatory networks, the former giving a preliminary overview of the system's global dynamics and the latter providing more detailed solutions. Another approach is to model biological regulatory networks as hybrid systems, i.e., systems which can display both continuous and discrete dynamic behaviors. Actually, the development of synthetic biology has shown that this is a suitable way to think about biological systems, which can often be constructed as networks with discrete controllers, and present hybrid behaviors. In this paper we discuss this approach as a special case of the reconfigurability paradigm, well studied in Computer Science (CS). In CS there are well developed computational tools to reason about hybrid systems. We argue that it is worth applying such tools in a biological context. One interesting tool is differential dynamic logic (dL), which has recently been developed by Platzer and applied to many case-studies. In this paper we discuss some simple examples of biological regulatory networks to illustrate how dL can be used as an alternative, or also as a complement to methods already used. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Biological and clinical dosimetry. Progress report July 1, 1964-June 30, 1979

    International Nuclear Information System (INIS)

    Laughlin, J.S.; McDonald, J.C.

    1979-01-01

    The dosimetric studies at this laboratory were initiated with the primary goal of developing systems for the determination of absorbed dose in biological research and clinical applications. The primary method under study is the local absorbed dose calorimeter, a concept initiated and developed by J. S. Laughlin. In addition, secondary dosimetric systems such as ionization chambers, chemical dosimeters and thermoluminescent dosimeters (TLD) are being developed and applied to provide an absolute basis for the evaluation and comparison of experiments, treatments, and other procedures using radiation

  2. Analysis and logical modeling of biological signaling transduction networks

    Science.gov (United States)

    Sun, Zhongyao

    The study of network theory and its application span across a multitude of seemingly disparate fields of science and technology: computer science, biology, social science, linguistics, etc. It is the intrinsic similarities embedded in the entities and the way they interact with one another in these systems that link them together. In this dissertation, I present from both the aspect of theoretical analysis and the aspect of application three projects, which primarily focus on signal transduction networks in biology. In these projects, I assembled a network model through extensively perusing literature, performed model-based simulations and validation, analyzed network topology, and proposed a novel network measure. The application of network modeling to the system of stomatal opening in plants revealed a fundamental question about the process that has been left unanswered in decades. The novel measure of the redundancy of signal transduction networks with Boolean dynamics by calculating its maximum node-independent elementary signaling mode set accurately predicts the effect of single node knockout in such signaling processes. The three projects as an organic whole advance the understanding of a real system as well as the behavior of such network models, giving me an opportunity to take a glimpse at the dazzling facets of the immense world of network science.

  3. The biological response of plucked human hair to low-dose radiation: a measure of individual radiosensitivity and a technique for biological dosimetry

    International Nuclear Information System (INIS)

    Swain, D.

    1997-01-01

    It is often assumed that the effects of radiation are linear with dose and that high dose effects can be extrapolated to low dose levels. However, there are a variety of mechanisms which can alter the response at low doses. The most important of these relate to induced sensitivity or induced repair mechanisms. It is therefore important that this area is studied in more depth by looking at the molecular effects and damage to cells at low doses. It is well known that there are certain rare genetic syndromes which predispose individuals to cancer, e.g. ataxia telangiectasia. It is also probable that there is a large range of sensitivity in the natural variation of individuals to the risk of radiation-induced cancer. It is proposed that radiosensitivity is studied using stimulated lymphocytes from whole blood and the technique extended to look at the effects in cell cultures established from human hair. Radiation treatment of cell cultures established from plucked human hair has been previously advocated as a non-invasive technique for non-uniform biological dosimetry and it is proposed that these techniques are adapted to the use of hair to estimate individual radiosensitivity. The aim is to establish and optimize these techniques for culturing keratinocytes from plucked human hair follicles with a view to study biological markers for the subsequent assessment of radiosensitivity. Preliminary results are promising and suggest that the technique for culturing keratinocytes from hair presents a feasible approach. Results from this primary cell culture technique and results from the comparison of the micronuclei data obtained from the cell cultures and stimulated lymphocytes will be presented. (author)

  4. Non-Hermitian localization in biological networks.

    Science.gov (United States)

    Amir, Ariel; Hatano, Naomichi; Nelson, David R

    2016-04-01

    We explore the spectra and localization properties of the N-site banded one-dimensional non-Hermitian random matrices that arise naturally in sparse neural networks. Approximately equal numbers of random excitatory and inhibitory connections lead to spatially localized eigenfunctions and an intricate eigenvalue spectrum in the complex plane that controls the spontaneous activity and induced response. A finite fraction of the eigenvalues condense onto the real or imaginary axes. For large N, the spectrum has remarkable symmetries not only with respect to reflections across the real and imaginary axes but also with respect to 90^{∘} rotations, with an unusual anisotropic divergence in the localization length near the origin. When chains with periodic boundary conditions become directed, with a systematic directional bias superimposed on the randomness, a hole centered on the origin opens up in the density-of-states in the complex plane. All states are extended on the rim of this hole, while the localized eigenvalues outside the hole are unchanged. The bias-dependent shape of this hole tracks the bias-independent contours of constant localization length. We treat the large-N limit by a combination of direct numerical diagonalization and using transfer matrices, an approach that allows us to exploit an electrostatic analogy connecting the "charges" embodied in the eigenvalue distribution with the contours of constant localization length. We show that similar results are obtained for more realistic neural networks that obey "Dale's law" (each site is purely excitatory or inhibitory) and conclude with perturbation theory results that describe the limit of large directional bias, when all states are extended. Related problems arise in random ecological networks and in chains of artificial cells with randomly coupled gene expression patterns.

  5. Emergence of communication in socio-biological networks

    CERN Document Server

    Berea, Anamaria

    2018-01-01

    This book integrates current advances in biology, economics of information and linguistics research through applications using agent-based modeling and social network analysis to develop scenarios of communication and language emergence in the social aspects of biological communications. The book presents a model of communication emergence that can be applied both to human and non-human living organism networks. The model is based on economic concepts and individual behavior fundamental for the study of trust and reputation networks in social science, particularly in economics; it is also based on the theory of the emergence of norms and historical path dependence that has been influential in institutional economics. Also included are mathematical models and code for agent-based models to explore various scenarios of language evolution, as well as a computer application that explores language and communication in biological versus social organisms, and the emergence of various meanings and grammars in human ...

  6. Cytogenetic biological dosimetry in radiological protection: chromosome aberration analysis in human lymphocyties

    International Nuclear Information System (INIS)

    Campos, I.M.A. de.

    1988-01-01

    The effects of ionizing radiation on chromosomes have been know for several decades and dose effect relationships are also fairly well established for several doses and dose rates. Apart from its biological significance, the interpretation of chromosome aberration frequency associated with human exposure to radiation plays an important role in dose assessment, particularly in cases where exposure is though to have occurred but no physical dose monitoring system was present. Based on the cytogenetic data obtained from seven cases of exposure to radiation the aberration frequency have been fitted to the quadratic function Y= αD + βD 2 as the dose response curves from literature. The dose equivalent estimate by frequency of chromosomic aberration found here was compared with 60 Co and 192 Ir already published curves obtained at almost similar dose rate together with some hematological data. (author) [pt

  7. Development and performance evaluation of a dynamic phantom for biological dosimetry of moving targets

    Science.gov (United States)

    Gemmel, A.; Bert, C.; Saito, N.; von Neubeck, C.; Iancu, G.; K-Weyrather, W.; Durante, M.; Rietzel, E.

    2010-06-01

    A dynamic phantom has been developed to allow for measurement of 3D cell survival distributions and the corresponding distributions of the RBE-weighted dose (RBED) in the presence of motion. The phantom consists of two 96-microwell plates holding Chinese hamster ovary cells inside a container filled with culture medium and is placed on a movable stage. Basic biological properties of the phantom were investigated without irradiation and after irradiation with a carbon ion beam, using both a stationary (reference) exposure and exposure during motion of the phantom perpendicular to the beam with beam tracking. There was no statistically significant difference between plating efficiency measured in the microwells with and without motion (0.75) and values reported in the literature. Mean differences between measured and calculated cell survival for these two irradiation modes were within ±5% of the target dose of 6 Gy (RBE).

  8. Development and performance evaluation of a dynamic phantom for biological dosimetry of moving targets

    Energy Technology Data Exchange (ETDEWEB)

    Gemmel, A; Bert, C; Saito, N; Von Neubeck, C; Iancu, G; K-Weyrather, W; Durante, M; Rietzel, E, E-mail: alexander.ag.gemmel@siemens.co [GSI Helmholtzzentrum fuer Schwerionenforschung, Planckstr 1, 64291 Darmstadt (Germany)

    2010-06-07

    A dynamic phantom has been developed to allow for measurement of 3D cell survival distributions and the corresponding distributions of the RBE-weighted dose (RBED) in the presence of motion. The phantom consists of two 96-microwell plates holding Chinese hamster ovary cells inside a container filled with culture medium and is placed on a movable stage. Basic biological properties of the phantom were investigated without irradiation and after irradiation with a carbon ion beam, using both a stationary (reference) exposure and exposure during motion of the phantom perpendicular to the beam with beam tracking. There was no statistically significant difference between plating efficiency measured in the microwells with and without motion (0.75) and values reported in the literature. Mean differences between measured and calculated cell survival for these two irradiation modes were within {+-}5% of the target dose of 6 Gy (RBE).

  9. Stopping powers for protons in materials of interest in dosimetry and in medical and biological applications

    International Nuclear Information System (INIS)

    Thwaites, D.I.

    1985-01-01

    Stopping powers are required for many radiation applications in medicine and biology. Their accuracy can be critical. Some published calculations for these situations have not included recent developments in stopping power theory or the body of work on deviations from additivity due to phase of chemical binding effects. These areas have recently been reviewed and mean excitation energies recommended for a range of materials of interest. Calculated stopping powers are presented for protons of 0.4 to 200 MeV taking the available information into account. The materials considered are Lucite, ICRU composition muscle and bone, A-150 plastic, a TE gas, acetylene and polystyrene and water and water vapour. With suitable corrections and suitable I values in the Bethe stopping power expression, accuracies of <2% can be achieved. (author)

  10. Analysis of the frequency of mutant T-helpers as a parameter for biological dosimetry

    International Nuclear Information System (INIS)

    Mel'nov, S.B.; Minenko, V.F.; Demidchik, E.P.

    1998-01-01

    It was made the attempt of quantitatively estimation of radiation damage by the frequency of mutant T-helpers, i.e. CD4+cells, depleted of T-cell receptor (TCR). The object of the study was lymphocytes of peripheral blood of children exposed to iodine radioisotopes therapy on medical indications. The examined group consisted of 36 patients 10 -21 years old, which were injected from 0,3 to 27,6 GBq of iodine 131. The time between exposition to iodine 131 and the investigation varied from 2 months to 3 years. The results gave evidence about the existence of direct relation between the frequency of mutant T-helpers and integrated dose. The character of the relation was described on the basis of mathematical processing. It was concluded that TCR-test can be used for restoration of the biological radiation dose

  11. Toward Petascale Biologically Plausible Neural Networks

    Science.gov (United States)

    Long, Lyle

    This talk will describe an approach to achieving petascale neural networks. Artificial intelligence has been oversold for many decades. Computers in the beginning could only do about 16,000 operations per second. Computer processing power, however, has been doubling every two years thanks to Moore's law, and growing even faster due to massively parallel architectures. Finally, 60 years after the first AI conference we have computers on the order of the performance of the human brain (1016 operations per second). The main issues now are algorithms, software, and learning. We have excellent models of neurons, such as the Hodgkin-Huxley model, but we do not know how the human neurons are wired together. With careful attention to efficient parallel computing, event-driven programming, table lookups, and memory minimization massive scale simulations can be performed. The code that will be described was written in C + + and uses the Message Passing Interface (MPI). It uses the full Hodgkin-Huxley neuron model, not a simplified model. It also allows arbitrary network structures (deep, recurrent, convolutional, all-to-all, etc.). The code is scalable, and has, so far, been tested on up to 2,048 processor cores using 107 neurons and 109 synapses.

  12. BiologicalNetworks 2.0 - an integrative view of genome biology data

    Directory of Open Access Journals (Sweden)

    Ponomarenko Julia

    2010-12-01

    Full Text Available Abstract Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other and their relations (interactions, co-expression, co-citations, and other. The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.

  13. Reproductive function and biological dosimetry prospective study of young thyroid differentiated cancer patients treated with I-131

    International Nuclear Information System (INIS)

    Di Giorgio, M.; Vallerga, M.B.; Taja, M.R.; Radl, A.; Chebel, Graciela; Fadel, Ana Maria; Gutierrez, Silvia; Normandi, Eduardo; Levalle, Oscar; Kundt, Miriam

    2011-01-01

    The administration of I-131 in the management of differentiated thyroid cancer (DTC) is a well established practice. As the spermatogonia is highly sensitive to radiation, large doses of internal radiation could result in adverse effects on reproductive function such as oligo/azoospermia and infertility. During spermiogenesis, mammalian chromatin undergoes replacement of nuclear histones by protamines, which yields a DNA sixfold more highly condensed in spermatozoa than in mitotic chromosomes. The structure of this highly packaged chromatin shows a low binding capacity for several fluorochromes and dyes such as chromomycin A3 (CMA3). The aim of this study is to assess the correlation between reproductive function (endocrine and exocrine testicular function, and levels of CMA3 stainability) and biological dosimetry in a prospective study of 4 young DTC patients treated with I-131. In this context, a background level of CMA3 binding in mature human sperm was established. It revealed a variable accessibility of CMA3 to the DNA that is dependant on packaging quality and thus, indicative of protamine deficiency. The identification of altered stainability suggests DNA damage as well as epigenetic effects, which may be indicators of male infertility. Transient impairment of spermatogenesis associated with an increase in FSH, an altered spermiogram and even azoospermia was observed after the administration of cumulative activities. Overall, testosterone levels were preserved, except in one case, which presented a drastically diminished value associated with an increase in LH level. As peripheral blood lymphocytes and spermatogonia have equivalent radiosensitivity (interphase death) we hypothesize that the knowledge of DNA damage recovery in peripheral lymphocytes could correlate with spermatogonia recovery and with FSH evolution. (authors)

  14. Reproductive function and biological dosimetry prospective study of young thyroid differentiated cancer patients treated with I-131

    International Nuclear Information System (INIS)

    Di Giorgio, Marina; Vallerga, Maria B.; Taja, Maria R.; Radl, Analia; Chebel, Graciela; Fadel, Ana M.; Gutierrez, Silvia; Normandi, Eduardo; Levalle, Oscar; Kundt, Miriam

    2008-01-01

    Full text: The administration of I-131 in the management of differentiated thyroid cancer (DTC) is a well established practice. As the spermatogonia is highly sensitive to radiation, large doses of internal radiation could result in adverse effects on reproductive function such as oligo/azoospermia and infertility. During spermiogenesis, mammalian chromatin undergoes replacement of nuclear histones by protamines, which yields a DNA sixfold more highly condensed in spermatozoa than in mitotic chromosomes. The structure of this highly packaged chromatin shows a low binding capacity for several fluoro chromes and dyes such as chromo mycin A 3 (CMA 3 ). The aim of this study is to assess the correlation between reproductive function (endocrine and exocrine testicular function, and levels of CMA 3 stainability) and biological dosimetry in a prospective study of 4 young DTC patients treated with I-131. In this context, a background level of CMA 3 binding in mature human sperm was established. It revealed a variable accessibility of CMA 3 to the DNA that is dependant on packaging quality and thus, indicative of protamine deficiency. The identification of altered stainability suggests DNA damage as well as epigenetic effects, which may be indicators of male infertility. Transient impairment of spermatogenesis associated with an increase in FSH, an altered spermiogram and even azoospermia was observed after the administration of cumulative activities. Overall, testosterone levels were preserved, except in one case, which presented a drastically diminished value associated with an increase in LH level. As peripheral blood lymphocytes and spermatogonia have equivalent radiosensitivity (interphase death) we hypothesize that the knowledge of DNA damage recovery in peripheral lymphocytes could correlate with spermatogonia recovery and with FSH evolution. Therefore, a prospective study on the decline of unstable chromosome aberrations is being conducted, considering the damage

  15. Neural network models: from biology to many - body phenomenology

    International Nuclear Information System (INIS)

    Clark, J.W.

    1993-01-01

    Theoretical work in neural networks has a strange feel for most physicists. In some cases the aspect of design becomes paramount. More comfortable ground at least for many body theorists may be found in realistic biological simulation, although the complexity of most problems is so awesome that incisive results will be hard won. It has also shown the impressive capabilities of artificial networks in pattern recognition and classification may be exploited to solve management problems in experimental physics and for discovery of radically new theoretical description of physical systems. This advance represents an important step towards the ultimate goal of neuro biological paradigm. (A.B.)

  16. GraphAlignment: Bayesian pairwise alignment of biological networks

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Meier, J.; Mustonen, V.; Lässig, M.; Berg, J.

    2012-01-01

    Roč. 6, November 21 (2012) ISSN 1752-0509 Grant - others:Deutsche Forschungsgemeinschaft(DE) SFB 680; Deutsche Forschungsgemeinschaft(DE) SFB-TR12; Deutsche Forschungsgemeinschaft(DE) BE 2478/2-1 Institutional research plan: CEZ:AV0Z50520514 Keywords : Graph alignment * Biological networks * Parameter estimation * Bioconductor Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.982, year: 2012

  17. Biological dosimetry of local radiation accidents of skin: possible cytological and biochemical methods

    International Nuclear Information System (INIS)

    Potten, C.S.

    1986-01-01

    Skin erythema or skin reaction is a highly dose-dependent change in skin appearance. A few gray can usually be detected in humans but higher doses are usually required for experimental rodents. The disadvantages are that the end-point is subjective and the response strongly influenced by numerous physical and biological factors. Changes in the levels of pigmentation can be detected in the epidermis and possibly the hair follicles but generally these only become apparent after chronic exposures. The skin appendages, particularly the hair follicles, could represent sensitive systems for detecting radiation exposures, but the cyclic behaviour of the hair follicles is difficult to control or determine in an accident. Acute cell death can be measured in the follicle germ and changes in the thickness and appearance of the hair are easily detected: in severe cases there is loss of hair (epilation). The number of dead cells per follicle section increased at a rate of 2.9/Gy and doses of about 0.2Gy can be easily detected. The width of the hair is reduced by about 7-8%/Gy and this change, which results in a dysplastic hair is believed to be the consequences of cell death in the follicles. (author)

  18. Enhancing Cytogenetic Biological Dosimetry Capabilities of the Philippines for Nuclear Incident Preparedness.

    Science.gov (United States)

    Asaad, Celia O; Caraos, Gloriamaris L; Robles, Gerardo Jose M; Asa, Anie Day D C; Cobar, Maria Lucia C; Asaad, Al-Ahmadgaid

    2016-01-01

    The utility of a biological dosimeter based on the analysis of dicentrics is invaluable in the event of a radiological emergency wherein the estimated absorbed dose of an exposed individual is crucial in the proper medical management of patients. The technique is also used for routine monitoring of occupationally exposed workers to determine radiation exposure. An in vitro irradiation study of human peripheral blood lymphocytes was conducted to establish a dose-response curve for radiation-induced dicentric aberrations. Blood samples were collected from volunteer donors and together with optically stimulated luminescence (OSL) dosimeters and were irradiated at 0, 0.1, 0.25, 0.5, 0.75, 1, 2, 4, and 6 Gy using a cobalt-60 radiotherapy unit. Blood samples were cultured for 48 h, and the metaphase chromosomes were prepared following the procedure of the International Atomic Energy Agency's Emergency Preparedness and Response - Biodosimetry 2011 manual. At least 100 metaphases were scored for dicentric aberrations at each dose point. The data were analyzed using R language program. The results indicated that the distribution of dicentric cells followed a Poisson distribution and the dose-response curve was established using the estimated model, Y dic = 0.0003 (±0.0003) +0.0336 (±0.0115) × D + 0.0236 (±0.0054) × D 2 . In this study, the reliability of the dose-response curve in estimating the absorbed dose was also validated for 2 and 4 Gy using OSL dosimeters. The data were fitted into the constructed curve. The result of the validation study showed that the obtained estimate for the absorbed exposure doses was close to the true exposure doses.

  19. Towards the understanding of network information processing in biology

    Science.gov (United States)

    Singh, Vijay

    Living organisms perform incredibly well in detecting a signal present in the environment. This information processing is achieved near optimally and quite reliably, even though the sources of signals are highly variable and complex. The work in the last few decades has given us a fair understanding of how individual signal processing units like neurons and cell receptors process signals, but the principles of collective information processing on biological networks are far from clear. Information processing in biological networks, like the brain, metabolic circuits, cellular-signaling circuits, etc., involves complex interactions among a large number of units (neurons, receptors). The combinatorially large number of states such a system can exist in makes it impossible to study these systems from the first principles, starting from the interactions between the basic units. The principles of collective information processing on such complex networks can be identified using coarse graining approaches. This could provide insights into the organization and function of complex biological networks. Here I study models of biological networks using continuum dynamics, renormalization, maximum likelihood estimation and information theory. Such coarse graining approaches identify features that are essential for certain processes performed by underlying biological networks. We find that long-range connections in the brain allow for global scale feature detection in a signal. These also suppress the noise and remove any gaps present in the signal. Hierarchical organization with long-range connections leads to large-scale connectivity at low synapse numbers. Time delays can be utilized to separate a mixture of signals with temporal scales. Our observations indicate that the rules in multivariate signal processing are quite different from traditional single unit signal processing.

  20. From biological and social network metaphors to coupled bio-social wireless networks

    Science.gov (United States)

    Barrett, Christopher L.; Eubank, Stephen; Anil Kumar, V.S.; Marathe, Madhav V.

    2010-01-01

    Biological and social analogies have been long applied to complex systems. Inspiration has been drawn from biological solutions to solve problems in engineering products and systems, ranging from Velcro to camouflage to robotics to adaptive and learning computing methods. In this paper, we present an overview of recent advances in understanding biological systems as networks and use this understanding to design and analyse wireless communication networks. We expand on two applications, namely cognitive sensing and control and wireless epidemiology. We discuss how our work in these two applications is motivated by biological metaphors. We believe that recent advances in computing and communications coupled with advances in health and social sciences raise the possibility of studying coupled bio-social communication networks. We argue that we can better utilise the advances in our understanding of one class of networks to better our understanding of the other. PMID:21643462

  1. Uncovering Biological Network Function via Graphlet Degree Signatures

    Directory of Open Access Journals (Sweden)

    Nataša Pržulj

    2008-01-01

    Full Text Available Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker’s yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.Results: We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein’s local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.Availability: Data is available upon request.

  2. Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks.

    Science.gov (United States)

    Tian, Ye; Zhang, Bai; Hoffman, Eric P; Clarke, Robert; Zhang, Zhen; Shih, Ie-Ming; Xuan, Jianhua; Herrington, David M; Wang, Yue

    2014-07-24

    Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific and dynamic in nature. To systematically characterize the selectively activated regulatory components and mechanisms, modeling tools must be able to effectively distinguish significant rewiring from random background fluctuations. While differential networks cannot be constructed by existing knowledge alone, novel incorporation of prior knowledge into data-driven approaches can improve the robustness and biological relevance of network inference. However, the major unresolved roadblocks include: big solution space but a small sample size; highly complex networks; imperfect prior knowledge; missing significance assessment; and heuristic structural parameter learning. To address these challenges, we formulated the inference of differential dependency networks that incorporate both conditional data and prior knowledge as a convex optimization problem, and developed an efficient learning algorithm to jointly infer the conserved biological network and the significant rewiring across different conditions. We used a novel sampling scheme to estimate the expected error rate due to "random" knowledge. Based on that scheme, we developed a strategy that fully exploits the benefit of this data-knowledge integrated approach. We demonstrated and validated the principle and performance of our method using synthetic datasets. We then applied our method to yeast cell line and breast cancer microarray data and obtained biologically plausible results. The open-source R software package and the experimental data are freely available at http://www.cbil.ece.vt.edu/software.htm. Experiments on both synthetic and real data demonstrate the effectiveness of the knowledge-fused differential dependency network in revealing the statistically significant rewiring in biological

  3. 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...

  4. Reachability Analysis in Probabilistic Biological Networks.

    Science.gov (United States)

    Gabr, Haitham; Todor, Andrei; Dobra, Alin; Kahveci, Tamer

    2015-01-01

    Extra-cellular molecules trigger a response inside the cell by initiating a signal at special membrane receptors (i.e., sources), which is then transmitted to reporters (i.e., targets) through various chains of interactions among proteins. Understanding whether such a signal can reach from membrane receptors to reporters is essential in studying the cell response to extra-cellular events. This problem is drastically complicated due to the unreliability of the interaction data. In this paper, we develop a novel method, called PReach (Probabilistic Reachability), that precisely computes the probability that a signal can reach from a given collection of receptors to a given collection of reporters when the underlying signaling network is uncertain. This is a very difficult computational problem with no known polynomial-time solution. PReach represents each uncertain interaction as a bi-variate polynomial. It transforms the reachability problem to a polynomial multiplication problem. We introduce novel polynomial collapsing operators that associate polynomial terms with possible paths between sources and targets as well as the cuts that separate sources from targets. These operators significantly shrink the number of polynomial terms and thus the running time. PReach has much better time complexity than the recent solutions for this problem. Our experimental results on real data sets demonstrate that this improvement leads to orders of magnitude of reduction in the running time over the most recent methods. Availability: All the data sets used, the software implemented and the alignments found in this paper are available at http://bioinformatics.cise.ufl.edu/PReach/.

  5. [Application of network biology on study of traditional Chinese medicine].

    Science.gov (United States)

    Tian, Sai-Sai; Yang, Jian; Zhao, Jing; Zhang, Wei-Dong

    2018-01-01

    With the completion of the human genome project, people have gradually recognized that the functions of the biological system are fulfilled through network-type interaction between genes, proteins and small molecules, while complex diseases are caused by the imbalance of biological processes due to a number of gene expression disorders. These have contributed to the rise of the concept of the "multi-target" drug discovery. Treatment and diagnosis of traditional Chinese medicine are based on holism and syndrome differentiation. At the molecular level, traditional Chinese medicine is characterized by multi-component and multi-target prescriptions, which is expected to provide a reference for the development of multi-target drugs. This paper reviews the application of network biology in traditional Chinese medicine in six aspects, in expectation to provide a reference to the modernized study of traditional Chinese medicine. Copyright© by the Chinese Pharmaceutical Association.

  6. Quantifying the connectivity of scale-free and biological networks

    Energy Technology Data Exchange (ETDEWEB)

    Shiner, J.S. E-mail: shiner@alumni.duke.edu; Davison, Matt E-mail: mdavison@uwo.ca

    2004-07-01

    Scale-free and biological networks follow a power law distribution p{sub k}{proportional_to}k{sup -{alpha}} for the probability that a node is connected to k other nodes; the corresponding ranges for {alpha} (biological: 1<{alpha}<2; scale-free: 2<{alpha}{<=}3) yield a diverging variance for the connectivity k and lack of predictability for the average connectivity. Predictability can be achieved with the Renyi, Tsallis and Landsberg-Vedral extended entropies and corresponding 'disorders' for correctly chosen values of the entropy index q. Escort distributions p{sub k}{proportional_to}k{sup -{alpha}}{sup q} with q>3/{alpha} also yield a nondiverging variance and predictability. It is argued that the Tsallis entropies may be the appropriate quantities for the study of scale-free and biological networks.

  7. Chromosomal analysis and application of biological dosimetry in two cases of apparent over exposure; Analisis cromosomico y aplicacion de la dosimetria biologica en dos casos de aparente sobreexposicion

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero C, C.; Brena V, M. [Departamento de Biologia, ININ A.P. 18-1027, 11801 Mexico D.F. (Mexico)

    2002-07-01

    The gamma radiation calibration curve of {sup 60} Co is used which was generated in the ININ Laboratory of Biology to calculate the exposure dose of two workers whose dosemeters marked values above of the limit allowed. The analysis indicates that in a first case, the aberrations frequency corresponded to the basal value, therefore there is not over exposure. The aberrations frequency of the second case is lightly above to the basal value and therefore the probability favors to what the physical dosimetry indicates. (Author)

  8. Fast grid layout algorithm for biological networks with sweep calculation.

    Science.gov (United States)

    Kojima, Kaname; Nagasaki, Masao; Miyano, Satoru

    2008-06-15

    Properly drawn biological networks are of great help in the comprehension of their characteristics. The quality of the layouts for retrieved biological networks is critical for pathway databases. However, since it is unrealistic to manually draw biological networks for every retrieval, automatic drawing algorithms are essential. Grid layout algorithms handle various biological properties such as aligning vertices having the same attributes and complicated positional constraints according to their subcellular localizations; thus, they succeed in providing biologically comprehensible layouts. However, existing grid layout algorithms are not suitable for real-time drawing, which is one of requisites for applications to pathway databases, due to their high-computational cost. In addition, they do not consider edge directions and their resulting layouts lack traceability for biochemical reactions and gene regulations, which are the most important features in biological networks. We devise a new calculation method termed sweep calculation and reduce the time complexity of the current grid layout algorithms through its encoding and decoding processes. We conduct practical experiments by using 95 pathway models of various sizes from TRANSPATH and show that our new grid layout algorithm is much faster than existing grid layout algorithms. For the cost function, we introduce a new component that penalizes undesirable edge directions to avoid the lack of traceability in pathways due to the differences in direction between in-edges and out-edges of each vertex. Java implementations of our layout algorithms are available in Cell Illustrator. masao@ims.u-tokyo.ac.jp Supplementary data are available at Bioinformatics online.

  9. Dosimetry Control: Technic and methods. Proceedings of the international workshop 'Actual problems of dosimetry'

    International Nuclear Information System (INIS)

    Lyutsko, A.M.; Nesterenko, V.B.; Chudakov, V.A.; Konoplya, E.F.; Milyutin, A.A.

    1997-10-01

    There is a number of unsolved problems of both dosimetric and radiometric control, questions of the biological dosimetry, reconstruction of dozes of irradiation of the population at radiation incidents, which require coordination of efforts of scientists in various areas of a science. The submitted materials are grouped on five units: dosimetry engineering, biological dosimetry and markers of radiation impact, dosimetry of a medical irradiation, normative and measurement assurance of the dosimetric control, monitoring and reconstruction of dozes at radiation incidents

  10. Dissecting the Molecular Mechanisms of Neurodegenerative Diseases through Network Biology

    Directory of Open Access Journals (Sweden)

    Jose A. Santiago

    2017-05-01

    Full Text Available Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease. In this review article, we highlight recent advances in network biology approaches with an emphasis in brain-networks that have provided insights into the molecular mechanisms leading to the most prevalent neurodegenerative diseases including Alzheimer’s (AD, Parkinson’s (PD and Huntington’s diseases (HD. We discuss how integrative approaches using multi-omics data from different tissues have been valuable for identifying biomarkers and therapeutic targets. In addition, we discuss the challenges the field of network medicine faces toward the translation of network-based findings into clinically actionable tools for personalized medicine applications.

  11. Dosimetry Service

    CERN Multimedia

    2006-01-01

    Cern Staff and Users can now consult their dose records for an individual or an organizational unit with HRT. Please see more information on our web page: http://cern.ch/rp-dosimetry Dosimetry Service is open every morning from 8.30 - 12.00. Closed in the afternoons. We would like to remind you that dosimeters cannot be sent to customers by internal mail. Short-term dosimeters (VCT's) must always be returned to the Service after the use and must not be left on the racks in the experimental areas or in the secretariats. Dosimetry Service Tel. 7 2155 Dosimetry.service@cern.ch http://cern.ch/rp-dosimetry

  12. Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Kim Man-Sun

    2012-05-01

    Full Text Available Abstract Background Network motifs provided a “conceptual tool” for understanding the functional principles of biological networks, but such motifs have primarily been used to consider static network structures. Static networks, however, cannot be used to reveal time- and region-specific traits of biological systems. To overcome this limitation, we proposed the concept of a “spatiotemporal network motif,” a spatiotemporal sequence of network motifs of sub-networks which are active only at specific time points and body parts. Results On the basis of this concept, we analyzed the developmental gene regulatory network of the Drosophila melanogaster embryo. We identified spatiotemporal network motifs and investigated their distribution pattern in time and space. As a result, we found how key developmental processes are temporally and spatially regulated by the gene network. In particular, we found that nested feedback loops appeared frequently throughout the entire developmental process. From mathematical simulations, we found that mutual inhibition in the nested feedback loops contributes to the formation of spatial expression patterns. Conclusions Taken together, the proposed concept and the simulations can be used to unravel the design principle of developmental gene regulatory networks.

  13. Biological dosimetry in astronauts

    International Nuclear Information System (INIS)

    Durante, M.

    1996-01-01

    Due to the unavoidable presence of ionizing radiation in space, astronauts are classified as radiation workers. I fact, dose rate in space is considerably higher than on earth. Radiation dose absorbed after one day in space is close to the dose received by all natural sources, excluding radon, in one year on earth. Large solar particle events can considerably increase this dose, and could even be life threatening for an inadequately protected crew

  14. Integrated Network Analysis and Effective Tools in Plant Systems Biology

    Directory of Open Access Journals (Sweden)

    Atsushi eFukushima

    2014-11-01

    Full Text Available One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype relationship in plant cellular systems. Integrated network analysis that combines omics data with mathematical models has received particular attention. Here we focus on the latest cutting-edge computational advances that facilitate their combination. We highlight (1 network visualization tools, (2 pathway analyses, (3 genome-scale metabolic reconstruction, and (4 the integration of high-throughput experimental data and mathematical models. Multi-omics data that contain the genome, transcriptome, proteome, and metabolome and mathematical models are expected to integrate and expand our knowledge of complex plant metabolisms.

  15. The impact of network biology in pharmacology and toxicology

    DEFF Research Database (Denmark)

    Panagiotou, Gianni; Taboureau, Olivier

    2012-01-01

    With the need to investigate alternative approaches and emerging technologies in order to increase drug efficacy and reduce adverse drug effects, network biology offers a novel way of approaching drug discovery by considering the effect of a molecule and protein's function in a global physiological...... and tools that allow integration and analysis of such information for understanding the properties of small molecules in the context of cellular networks. With the recent advances in the omics area, global integrative approaches are necessary to cope with the massive amounts of data, and biomedical...

  16. Biologically-inspired Learning in Pulsed Neural Networks

    DEFF Research Database (Denmark)

    Lehmann, Torsten; Woodburn, Robin

    1999-01-01

    Self-learning chips to implement many popular ANN (artificial neural network) algorithms are very difficult to design. We explain why this is so and say what lessons previous work teaches us in the design of self-learning systems. We offer a contribution to the `biologically-inspired' approach......, explaining what we mean by this term and providing an example of a robust, self-learning design that can solve simple classical-conditioning tasks. We give details of the design of individual circuits to perform component functions, which can then be combined into a network to solve the task. We argue...

  17. The status of the seventh report in the series Biological Effects of Ionizing Radiations and a revised dosimetry for the Radiation Effects Research Foundation's A-bomb studies

    International Nuclear Information System (INIS)

    Douple, Evan; Jostes, Rick

    2002-01-01

    Results of a National Academies workshop and feasibility study led US Governmental agencies to request the Board on Radiation Effects Research of the National Research Council to commence a risk assessment study in 1998 as the seventh report in the series Biological Effects of Ionizing Radiations (BEIR VII). Originally targeted for completion in the autumn of 2001, the study Potential Health Effects of Exposure to Low Dose, Low-LET Ionizing Radiation was extended until the autumn of 2003 at the request of the sponsors. Two factors contributing to this decision are discussed: a revised dosimetry to update DS86 for the Radiation Effects Research Foundation's A-bomb-survivor studies and the potential for new information to become available from low-dose studies that are under way. Epidemiological and biological data since BEIR V are being considered by a BEIR VII committee composed of 17 members. The committee's statement of task is reviewed along with the major recommendations of the recent National Research Council report on the status of DS86 - recommendations that are being implemented by US and Japan dosimetry working groups. (author)

  18. Modeling Cancer Metastasis using Global, Quantitative and Integrative Network Biology

    DEFF Research Database (Denmark)

    Schoof, Erwin; Erler, Janine

    understanding of molecular processes which are fundamental to tumorigenesis. In Article 1, we propose a novel framework for how cancer mutations can be studied by taking into account their effect at the protein network level. In Article 2, we demonstrate how global, quantitative data on phosphorylation dynamics...... can be generated using MS, and how this can be modeled using a computational framework for deciphering kinase-substrate dynamics. This framework is described in depth in Article 3, and covers the design of KinomeXplorer, which allows the prediction of kinases responsible for modulating observed...... phosphorylation dynamics in a given biological sample. In Chapter III, we move into Integrative Network Biology, where, by combining two fundamental technologies (MS & NGS), we can obtain more in-depth insights into the links between cellular phenotype and genotype. Article 4 describes the proof...

  19. Analysis of complex networks from biology to linguistics

    CERN Document Server

    Dehmer, Matthias

    2009-01-01

    Mathematical problems such as graph theory problems are of increasing importance for the analysis of modelling data in biomedical research such as in systems biology, neuronal network modelling etc. This book follows a new approach of including graph theory from a mathematical perspective with specific applications of graph theory in biomedical and computational sciences. The book is written by renowned experts in the field and offers valuable background information for a wide audience.

  20. Biological dosimetry of ionizing radiation by chromosomal aberration analysis; Dosimetria biologica de las radiaciones ionizantes mediante el analisis de aberraciones cromosomicas

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Castano, S.; Silva, A.; Navlet, J.

    1990-07-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical, and cytogenetic data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable. In this case, the study ol chromosomal aberrations, normally dicentric chromosomes, in peripheral lymphocytes can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using dicentric chromosomes analysis, X-rays at 300 kVp, 114 rad/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y ={alpha} + {beta}{sub 1}D + {beta}{sub 2}D 2 , where Y is the number of dicentrics per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 14 refs.

  1. FiBi - A French network of facilities for irradiation in biology: The organisation of the network and the research opportunities associated

    International Nuclear Information System (INIS)

    Gaillard-Lecanu, E.; Coffigny, H.; Poncy, J.L.; Authier, N.; Verrey, B.; Bailly, I.; Baldacchino, G.; Bordy, J.M.; Carriere, M.; Leplat, J.J.; Pin, S.; Pommeret, S.; Thuret, J.Y.; Renault, J.P.; Cortella, I.; Duval, D.; Khodja, H.; Testard, I.

    2006-01-01

    The Life Science Division of the Atomic Energy Commission has developed a national network of available irradiation facilities for biological studies. One aim is to optimise the irradiation of biological samples, through a compendium of existing facilities allowing for the preserving and the irradiation of these samples in good conditions, and for providing an appropriate and reliable dosimetry. Given the high cost of the facilities and their specialization (nature and precision of irradiation on a cell scale, dose and dose rate), closeness is no longer the only criteria of choice for biologists. Development is leaning towards the implementation of irradiation platforms gathering irradiation tools associated with specific methods belonging to biology: cell culture, molecular biology and even animal care houses. The aim is to be able to offer biologists the most appropriate experimental tools, and to modify them according to the changing needs of radiobiology. This work is currently in progress and the database is still not exhaustive and shall be implemented as and when new documents are drawn up and new facilities are opened. (author)

  2. Impact of heuristics in clustering large biological networks.

    Science.gov (United States)

    Shafin, Md Kishwar; Kabir, Kazi Lutful; Ridwan, Iffatur; Anannya, Tasmiah Tamzid; Karim, Rashid Saadman; Hoque, Mohammad Mozammel; Rahman, M Sohel

    2015-12-01

    Traditional clustering algorithms often exhibit poor performance for large networks. On the contrary, greedy algorithms are found to be relatively efficient while uncovering functional modules from large biological networks. The quality of the clusters produced by these greedy techniques largely depends on the underlying heuristics employed. Different heuristics based on different attributes and properties perform differently in terms of the quality of the clusters produced. This motivates us to design new heuristics for clustering large networks. In this paper, we have proposed two new heuristics and analyzed the performance thereof after incorporating those with three different combinations in a recently celebrated greedy clustering algorithm named SPICi. We have extensively analyzed the effectiveness of these new variants. The results are found to be promising. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Detecting and evaluating communities in complex human and biological networks

    Science.gov (United States)

    Morrison, Greg; Mahadevan, L.

    2012-02-01

    We develop a simple method for detecting the community structure in a network can by utilizing a measure of closeness between nodes. This approach readily leads to a method of coarse graining the network, which allows the detection of the natural hierarchy (or hierarchies) of community structure without appealing to an unknown resolution parameter. The closeness measure can also be used to evaluate the robustness of an individual node's assignment to its community (rather than evaluating only the quality of the global structure). Each of these methods in community detection and evaluation are illustrated using a variety of real world networks of either biological or sociological importance and illustrate the power and flexibility of the approach.

  4. Perturbation Biology: Inferring Signaling Networks in Cellular Systems

    Science.gov (United States)

    Miller, Martin L.; Gauthier, Nicholas P.; Jing, Xiaohong; Kaushik, Poorvi; He, Qin; Mills, Gordon; Solit, David B.; Pratilas, Christine A.; Weigt, Martin; Braunstein, Alfredo; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2013-01-01

    We present a powerful experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be useful in the design of combinatorial therapy against cancer. The experiments are systematic series of perturbations of cancer cell lines by targeted drugs, singly or in combination. The response to perturbation is quantified in terms of relative changes in the measured levels of proteins, phospho-proteins and cellular phenotypes such as viability. Computational network models are derived de novo, i.e., without prior knowledge of signaling pathways, and are based on simple non-linear differential equations. The prohibitively large solution space of all possible network models is explored efficiently using a probabilistic algorithm, Belief Propagation (BP), which is three orders of magnitude faster than standard Monte Carlo methods. Explicit executable models are derived for a set of perturbation experiments in SKMEL-133 melanoma cell lines, which are resistant to the therapeutically important inhibitor of RAF kinase. The resulting network models reproduce and extend known pathway biology. They empower potential discoveries of new molecular interactions and predict efficacious novel drug perturbations, such as the inhibition of PLK1, which is verified experimentally. This technology is suitable for application to larger systems in diverse areas of molecular biology. PMID:24367245

  5. Physical limits of feedback noise-suppression in biological networks

    International Nuclear Information System (INIS)

    Zhang, Jiajun; Yuan, Zhanjiang; Zhou, Tianshou

    2009-01-01

    Feedback is a ubiquitous control mechanism of biological networks, and has also been identified in a variety of regulatory systems and organisms. It has been shown that, for a given gain and with negligible intrinsic noise, negative feedback impairs noise buffering whereas positive feedback enhances noise buffering. We further investigate the influence of negative and positive feedback on noise in output signals by considering both intrinsic and extrinsic noise as well as operator noise. We find that, while maintaining the system sensitivity, either there exists a minimum of the output noise intensity corresponding to a biologically feasible feedback strength, or the output noise intensity is a monotonic function of feedback strength bounded by both biological and dynamical constraints. In both cases, feedback noise-suppression is physically limited. In other words, noise suppressed by negative or positive feedback cannot be reduced without limitation even in the case of slow transcription

  6. From biological neural networks to thinking machines: Transitioning biological organizational principles to computer technology

    Science.gov (United States)

    Ross, Muriel D.

    1991-01-01

    The three-dimensional organization of the vestibular macula is under study by computer assisted reconstruction and simulation methods as a model for more complex neural systems. One goal of this research is to transition knowledge of biological neural network architecture and functioning to computer technology, to contribute to the development of thinking computers. Maculas are organized as weighted neural networks for parallel distributed processing of information. The network is characterized by non-linearity of its terminal/receptive fields. Wiring appears to develop through constrained randomness. A further property is the presence of two main circuits, highly channeled and distributed modifying, that are connected through feedforward-feedback collaterals and biasing subcircuit. Computer simulations demonstrate that differences in geometry of the feedback (afferent) collaterals affects the timing and the magnitude of voltage changes delivered to the spike initiation zone. Feedforward (efferent) collaterals act as voltage followers and likely inhibit neurons of the distributed modifying circuit. These results illustrate the importance of feedforward-feedback loops, of timing, and of inhibition in refining neural network output. They also suggest that it is the distributed modifying network that is most involved in adaptation, memory, and learning. Tests of macular adaptation, through hyper- and microgravitational studies, support this hypothesis since synapses in the distributed modifying circuit, but not the channeled circuit, are altered. Transitioning knowledge of biological systems to computer technology, however, remains problematical.

  7. Biological instability in a chlorinated drinking water distribution network.

    Science.gov (United States)

    Nescerecka, Alina; Rubulis, Janis; Vital, Marius; Juhna, Talis; Hammes, Frederik

    2014-01-01

    The purpose of a drinking water distribution system is to deliver drinking water to the consumer, preferably with the same quality as when it left the treatment plant. In this context, the maintenance of good microbiological quality is often referred to as biological stability, and the addition of sufficient chlorine residuals is regarded as one way to achieve this. The full-scale drinking water distribution system of Riga (Latvia) was investigated with respect to biological stability in chlorinated drinking water. Flow cytometric (FCM) intact cell concentrations, intracellular adenosine tri-phosphate (ATP), heterotrophic plate counts and residual chlorine measurements were performed to evaluate the drinking water quality and stability at 49 sampling points throughout the distribution network. Cell viability methods were compared and the importance of extracellular ATP measurements was examined as well. FCM intact cell concentrations varied from 5×10(3) cells mL(-1) to 4.66×10(5) cells mL(-1) in the network. While this parameter did not exceed 2.1×10(4) cells mL(-1) in the effluent from any water treatment plant, 50% of all the network samples contained more than 1.06×10(5) cells mL(-1). This indisputably demonstrates biological instability in this particular drinking water distribution system, which was ascribed to a loss of disinfectant residuals and concomitant bacterial growth. The study highlights the potential of using cultivation-independent methods for the assessment of chlorinated water samples. In addition, it underlines the complexity of full-scale drinking water distribution systems, and the resulting challenges to establish the causes of biological instability.

  8. PREFACE: Complex Networks: from Biology to Information Technology

    Science.gov (United States)

    Barrat, A.; Boccaletti, S.; Caldarelli, G.; Chessa, A.; Latora, V.; Motter, A. E.

    2008-06-01

    The field of complex networks is one of the most active areas in contemporary statistical physics. Ten years after seminal work initiated the modern study of networks, interest in the field is in fact still growing, as indicated by the ever increasing number of publications in network science. The reason for such a resounding success is most likely the simplicity and broad significance of the approach that, through graph theory, allows researchers to address a variety of different complex systems within a common framework. This special issue comprises a selection of contributions presented at the workshop 'Complex Networks: from Biology to Information Technology' held in July 2007 in Pula (Cagliari), Italy as a satellite of the general conference STATPHYS23. The contributions cover a wide range of problems that are currently among the most important questions in the area of complex networks and that are likely to stimulate future research. The issue is organised into four sections. The first two sections describe 'methods' to study the structure and the dynamics of complex networks, respectively. After this methodological part, the issue proceeds with a section on applications to biological systems. The issue closes with a section concentrating on applications to the study of social and technological networks. The first section, entitled Methods: The Structure, consists of six contributions focused on the characterisation and analysis of structural properties of complex networks: The paper Motif-based communities in complex networks by Arenas et al is a study of the occurrence of characteristic small subgraphs in complex networks. These subgraphs, known as motifs, are used to define general classes of nodes and their communities by extending the mathematical expression of the Newman-Girvan modularity. The same line of research, aimed at characterising network structure through the analysis of particular subgraphs, is explored by Bianconi and Gulbahce in Algorithm

  9. Use artificial neural network to align biological ontologies.

    Science.gov (United States)

    Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

    2008-09-16

    Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

  10. Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

    Directory of Open Access Journals (Sweden)

    Martin Florian

    2012-05-01

    Full Text Available Abstract Background High-throughput measurement technologies produce data sets that have the potential to elucidate the biological impact of disease, drug treatment, and environmental agents on humans. The scientific community faces an ongoing challenge in the analysis of these rich data sources to more accurately characterize biological processes that have been perturbed at the mechanistic level. Here, a new approach is built on previous methodologies in which high-throughput data was interpreted using prior biological knowledge of cause and effect relationships. These relationships are structured into network models that describe specific biological processes, such as inflammatory signaling or cell cycle progression. This enables quantitative assessment of network perturbation in response to a given stimulus. Results Four complementary methods were devised to quantify treatment-induced activity changes in processes described by network models. In addition, companion statistics were developed to qualify significance and specificity of the results. This approach is called Network Perturbation Amplitude (NPA scoring because the amplitudes of treatment-induced perturbations are computed for biological network models. The NPA methods were tested on two transcriptomic data sets: normal human bronchial epithelial (NHBE cells treated with the pro-inflammatory signaling mediator TNFα, and HCT116 colon cancer cells treated with the CDK cell cycle inhibitor R547. Each data set was scored against network models representing different aspects of inflammatory signaling and cell cycle progression, and these scores were compared with independent measures of pathway activity in NHBE cells to verify the approach. The NPA scoring method successfully quantified the amplitude of TNFα-induced perturbation for each network model when compared against NF-κB nuclear localization and cell number. In addition, the degree and specificity to which CDK

  11. Phylogenetically informed logic relationships improve detection of biological network organization

    Science.gov (United States)

    2011-01-01

    Background A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses. Results Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks. Conclusion Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction. PMID:22172058

  12. Biological dosimetry after criticality accidents. Intercomparison exercise in the Silene Reactor - France; Dosimetria biologica en accidentes de criticidad. Ejercicio de intercomparacion en el Reactor Silene - Francia

    Energy Technology Data Exchange (ETDEWEB)

    Di Giorgio, Marina; Vallerga, Maria B; Taja, Maria R [Autoridad Regulatoria Nuclear, Buenos Aires (Argentina); arn gov ar, E-mail: mdigiorg@cae

    2004-07-01

    The Institute of Radiation Protection and Nuclear Safety Institute (IRSN) organized an international biological dosimetry intercomparison, at the SILENE experimental reactor (Valduc, France), simulating different criticality scenarios: bare source 4 Gy, lead shield source 1 and 2 Gy and gamma pure {sup 60}Co source 2 Gy. Fifteen laboratories were involved in this exercise, including the Argentine Biological Dosimetry Laboratory. The purposes of the intercomparison were: 1) To compare the unstable chromosome aberration (UCA) frequency observed by the different laboratories; and 2) To compare the dose estimation for gamma rays and neutrons. The objects of the present work were: I) To compare the mean frequency of UCA observed by the Argentine laboratory with the mean frequency observed by the participant laboratories as a whole. II) To compare the dose estimates performed by the Argentine lab with those estimated by the other laboratories involved in the second stage of the intercomparison. Overall, the mean frequencies of UCA and the correspondent 95% confidence limits obtained by the Argentine lab were consistent with the results obtained by the laboratories as a whole. For the gamma pure scenario, smaller variations were observed among laboratories in terms of dose (CV=18,2%) than in terms of frequency (CV=30,1%). For the mixed field scenarios, only four laboratories, including the Argentine lab, estimated gamma and neutron components of the total dose and just two (Argentine lab and lab 12) were in agreement with the given physical doses. The 1 Gy experiment presented lesser variations both in terms of frequency and dose than the other two scenarios. For the 4 and 2 Gy experiments, variations in neutron dose were more significant than variations in gamma dose, related to the magnitude of the dose. The results suggest that intercomparison exercises jointly with the accreditation of biological dosimetry by cytogenetic service laboratories, in compliance with ISO

  13. ESR Dosimetry

    International Nuclear Information System (INIS)

    Baffa, Oswaldo; Rossi, Bruno; Graeff, Carlos; Kinoshita, Angela; Chen Abrego, Felipe; Santos, Adevailton Bernardo dos

    2004-01-01

    ESR dosimetry is widely used for several applications such as dose assessment in accidents, medical applications and sterilization of food and other materials. In this work the dosimetric properties of natural and synthetic Hydroxyapatite, Alanine, and 2-Methylalanine are presented. Recent results on the use of a K-Band (24 GHz) ESR spectrometer in dosimetry are also presented

  14. Dosimetry Service

    CERN Multimedia

    2005-01-01

    Please remember to read your dosimeter at least once a month. Regular read-outs are vital to ensure that your personal dose is periodically monitored. Dosimeters should be read even if you have not visited the controlled areas. Dosimetry Service - Tel. 7 2155 http://cern.ch/rp-dosimetry

  15. Dosimetry Service

    CERN Multimedia

    Dosimetry Service

    2005-01-01

    Please remember to read your dosimeter at least once a month. Regular read-outs are vital to ensure that your personal dose is periodically monitored. Dosimeters should be read even if you have not visited the controlled areas. Dosimetry Service Tel. 7 2155 http://cern.ch/rp-dosimetry

  16. Dosimetry Service

    CERN Multimedia

    2005-01-01

    Please remember to read your dosimeter at least once a month. Regular read-outs are vital to ensure that your personal dose is periodically monitored. Dosimeters should be read even if you have not visited the controlled areas. Dosimetry Service - Tel. 72155 http://cern.ch/rp-dosimetry

  17. Biological dosimetry of patients with differenced carcinoma of thyroid treated with Iodine-131; Dosimetria biologica de pacientes con carcinoma diferenciado de tiroides tratados con Iodo-131

    Energy Technology Data Exchange (ETDEWEB)

    Vallerga, M. B.; Rojo, A.M.; Taja, M.R.; Deluca, G.; Di Giorgio, M. [Autoridad Regulatoria Nuclear Av. Del Libertador 8250 (C1429BNP). Buenos Aires (Argentina); Fadel, A. [Hospital General de Agudos Dr. Carlos Durand Av. Diaz Velez 5044. Buenos Aires (Argentina); Cabrejas, M.; Valdivieso, C. [Hospital de Clfnicas Jose de San Martin Av. Cordoba 2351 (CP1120). Buenos Aires (Argentina)]. e-mail: mvallerg@cae.arn.gov.ar

    2006-07-01

    The administration of I-131 to patient with Differentiated Thyroid Carcinoma (CaDiT) it is used inside the therapeutic outline as later step to the thyroidectomy. However, the good activity to give is of difficult determination due to factors such as, the variability in the capacity of tumoral reception of the I-131, distribution of the pharmaceutical, physiologic status, other associate pathologies, grade of advance of the illness, and previous treatments. Additionally, the activity to administer is dependent of the dose of tolerance in the healthy tissues; superior dose to 2 Gy in bone marrow, its could drive to myelotoxicity. At the moment, the form more extended of administration it is the empiric prescription that considers clinical parameters and of laboratory for their determination. Presently work, the protocol of applied treatment incorporates the evaluation for internal dosimetry and biological dosimetry to estimate absorbed dose in bone marrow. The biological estimate of the dose of these patients is based on the quantification of chromosomal aberrations whose frequency is referred to a curve-dose response in which the lymphocytes is irradiated in vitro with I-131, allowing to determine the in vivo dose to the patient's circulating lymphocytes. The objective of the present work is to determine the applicability of different cytogenetic essays in the estimate of the absorbed dose to the whole body or specific organs. Three patients were evaluated with CaDiT. Their treatment protocol consisted on a tracer administration of radioactive iodine of 74 - 111 MBq (2 - 3 mCi) and a therapy 7,4 - 11,1 GBq (200 - 300 mCi). Previous to the tracer administration and 8 days post-therapeutic administration took samples of veined blood that were evaluated by biological dosimetry by means of the application of the techniques: conventional cytogenetic Micronucleus and FISH (Hybridization in situ by Fluorescence). Starting from the frequencies of observed chromosomal

  18. Color encoding in biologically-inspired convolutional neural networks.

    Science.gov (United States)

    Rafegas, Ivet; Vanrell, Maria

    2018-05-11

    Convolutional Neural Networks have been proposed as suitable frameworks to model biological vision. Some of these artificial networks showed representational properties that rival primate performances in object recognition. In this paper we explore how color is encoded in a trained artificial network. It is performed by estimating a color selectivity index for each neuron, which allows us to describe the neuron activity to a color input stimuli. The index allows us to classify whether they are color selective or not and if they are of a single or double color. We have determined that all five convolutional layers of the network have a large number of color selective neurons. Color opponency clearly emerges in the first layer, presenting 4 main axes (Black-White, Red-Cyan, Blue-Yellow and Magenta-Green), but this is reduced and rotated as we go deeper into the network. In layer 2 we find a denser hue sampling of color neurons and opponency is reduced almost to one new main axis, the Bluish-Orangish coinciding with the dataset bias. In layers 3, 4 and 5 color neurons are similar amongst themselves, presenting different type of neurons that detect specific colored objects (e.g., orangish faces), specific surrounds (e.g., blue sky) or specific colored or contrasted object-surround configurations (e.g. blue blob in a green surround). Overall, our work concludes that color and shape representation are successively entangled through all the layers of the studied network, revealing certain parallelisms with the reported evidences in primate brains that can provide useful insight into intermediate hierarchical spatio-chromatic representations. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. CellNet: Network Biology Applied to Stem Cell Engineering

    Science.gov (United States)

    Cahan, Patrick; Li, Hu; Morris, Samantha A.; da Rocha, Edroaldo Lummertz; Daley, George Q.; Collins, James J.

    2014-01-01

    SUMMARY Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population, and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. PMID:25126793

  20. Qualitative reasoning for biological network inference from systematic perturbation experiments.

    Science.gov (United States)

    Badaloni, Silvana; Di Camillo, Barbara; Sambo, Francesco

    2012-01-01

    The systematic perturbation of the components of a biological system has been proven among the most informative experimental setups for the identification of causal relations between the components. In this paper, we present Systematic Perturbation-Qualitative Reasoning (SPQR), a novel Qualitative Reasoning approach to automate the interpretation of the results of systematic perturbation experiments. Our method is based on a qualitative abstraction of the experimental data: for each perturbation experiment, measured values of the observed variables are modeled as lower, equal or higher than the measurements in the wild type condition, when no perturbation is applied. The algorithm exploits a set of IF-THEN rules to infer causal relations between the variables, analyzing the patterns of propagation of the perturbation signals through the biological network, and is specifically designed to minimize the rate of false positives among the inferred relations. Tested on both simulated and real perturbation data, SPQR indeed exhibits a significantly higher precision than the state of the art.

  1. Molecular codes in biological and chemical reaction networks.

    Directory of Open Access Journals (Sweden)

    Dennis Görlich

    Full Text Available Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio- chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries, biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades, an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

  2. Validation of an immunochemical assay for the detection of DNA damage as a tool for biological dosimetry of human exposure to ionizing radiation

    International Nuclear Information System (INIS)

    Schans, G.P. van der; Timmerman, A.J.; Wojewodzka, M.; Zaim, J.

    1997-01-01

    A method for biological dosimetry based on the immunochemical detection of DNA damage in human white blood cells has been validated. To this end the method developed at TNO (Rijswijk, the Netherlands) was also set up at INCT (Warsaw, Poland). Blood samples of 11 individuals were irradiated with 0 or 5 Gy of 170 kV X-rays at INCT and analyzed both at INCT and TNO. It appeared that in both laboratories damage could be detected to the same extent. The average background level of DNA damage amounted to 1.0 Gy-eq with an interindividual standard deviation of 0.25 Gy. The contribution of the sample variance to the total variance is only 14%. The radiosensitivity showed only a variation of about 10% and can, therefore, be neglected in estimating the radiation dose from the amount of DNA damage detected. (author)

  3. Spectrometry and dosimetry of isotopic sources of neutrons by means of artificial neural networks

    International Nuclear Information System (INIS)

    Vega C, H. R.; Ortiz R, J. M.; Hernandez D, V. M; Martinez B, M. R.; Gallego, E.; Lorente, A.; Barquero, R.

    2010-09-01

    The artificial neural networks technology has been applied to reconstruct the neutrons spectra of two isotopic sources: 252 Cf, and 241 Am-Be. Also, this technology has been applied to obtain the effective dose, E, and the personal dose equivalents, Hp(10) and environmental, H *(10). To obtain the spectra and the doses only were used the count rates produced in a Bonner Spheres spectrometer with a scintillator of 6 LiI(Eu) of 0.4 φ x 0.4 cm 2 . The equivalent environmental dose and the spectra of the sources were also obtained by means of the reconstruction code BUNKIUT. When comparing the results obtained by means of both procedures it was found that they are consistent. (Author)

  4. 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.

  5. A European network of experts with direct responsibility for monitoring and dosimetry after a deliberate release of radioactive material or a deliberate radiation exposure

    International Nuclear Information System (INIS)

    Rahola, Tua; Muikku, Maarit; Pellow, Peter G.D.; Etherington, George; Hodgson, Alan; Youngman, Mike J.; Le Guen, Bernard; Berard, Philippe; Lopez, Maria A.

    2008-01-01

    In the event of an accidental or deliberate release of radionuclides to the environment, individual monitoring and dose assessment may be needed for large numbers of people. The consequences of such incidents are not limited by national boundaries. However, within the European Union (EU), there has not been any coordinated strategy for individual monitoring and dose assessment. CONRAD (CO-ordination Action for Radiation Dosimetry) is an EC 6 th Framework Programme Co-ordination Action sponsored by EURADOS (the European Radiation Dosimetry Group, http://www.eurados.org). The objective of Task 5.4 of Work Package 5 of the CONRAD project, coordinated by HPA (UK) and STUK (Finland), is the development of a network of people and organisations with responsibilities for emergency monitoring of emergency services personnel and members of the public. The network (named EUREMON) aims to promote sharing of information between countries on plans and arrangements for individual monitoring. It currently has 51 individual members from 22 EU countries, 8 non-EU countries and two international organisations. After it was established, the network was used in a survey of plans and arrangements for emergency personal monitoring in EU countries. Information is also being compiled on portable and transportable monitoring facilities and equipment in the EU. (author)

  6. Quantum Processes and Dynamic Networks in Physical and Biological Systems.

    Science.gov (United States)

    Dudziak, Martin Joseph

    Quantum theory since its earliest formulations in the Copenhagen Interpretation has been difficult to integrate with general relativity and with classical Newtonian physics. There has been traditionally a regard for quantum phenomena as being a limiting case for a natural order that is fundamentally classical except for microscopic extrema where quantum mechanics must be applied, more as a mathematical reconciliation rather than as a description and explanation. Macroscopic sciences including the study of biological neural networks, cellular energy transports and the broad field of non-linear and chaotic systems point to a quantum dimension extending across all scales of measurement and encompassing all of Nature as a fundamentally quantum universe. Theory and observation lead to a number of hypotheses all of which point to dynamic, evolving networks of fundamental or elementary processes as the underlying logico-physical structure (manifestation) in Nature and a strongly quantized dimension to macroscalar processes such as are found in biological, ecological and social systems. The fundamental thesis advanced and presented herein is that quantum phenomena may be the direct consequence of a universe built not from objects and substance but from interacting, interdependent processes collectively operating as sets and networks, giving rise to systems that on microcosmic or macroscopic scales function wholistically and organically, exhibiting non-locality and other non -classical phenomena. The argument is made that such effects as non-locality are not aberrations or departures from the norm but ordinary consequences of the process-network dynamics of Nature. Quantum processes are taken to be the fundamental action-events within Nature; rather than being the exception quantum theory is the rule. The argument is also presented that the study of quantum physics could benefit from the study of selective higher-scale complex systems, such as neural processes in the brain

  7. Foundations of ionizing radiation dosimetry

    International Nuclear Information System (INIS)

    Denisenko, O.N.; Pereslegin, I.A.

    1985-01-01

    Foundations of dosimetry in application to radiotherapy are presented. General characteristics of ionizing radiations and main characteristics of ionizing radiation sources, mostly used in radiotherapy, are given. Values and units for measuring ionizing radiation (activity of a radioactive substance, absorbed dose, exposure dose, integral dose and dose equivalent are considered. Different methods and instruments for ionizing radiation dosimetry are discussed. The attention is paid to the foundations of clinical dosimetry (representation of anatomo-topographic information, choice of radiation conditions, realization of radiation methods, corrections for a configuration and inhomogeneity of a patient's body, account of biological factors of radiation effects, instruments of dose field formation, control of irradiation procedure chosen)

  8. Notes on a PDE system for biological network formation

    KAUST Repository

    Haskovec, Jan

    2016-01-22

    We present new analytical and numerical results for the elliptic–parabolic system of partial differential equations proposed by Hu and Cai, which models the formation of biological transport networks. The model describes the pressure field using a Darcy’s type equation and the dynamics of the conductance network under pressure force effects. Randomness in the material structure is represented by a linear diffusion term and conductance relaxation by an algebraic decay term. The analytical part extends the results of Haskovec et al. (2015) regarding the existence of weak and mild solutions to the whole range of meaningful relaxation exponents. Moreover, we prove finite time extinction or break-down of solutions in the spatially one-dimensional setting for certain ranges of the relaxation exponent. We also construct stationary solutions for the case of vanishing diffusion and critical value of the relaxation exponent, using a variational formulation and a penalty method. The analytical part is complemented by extensive numerical simulations. We propose a discretization based on mixed finite elements and study the qualitative properties of network structures for various parameter values. Furthermore, we indicate numerically that some analytical results proved for the spatially one-dimensional setting are likely to be valid also in several space dimensions.

  9. Neutron spectrometry and dosimetry by means of evolutive neural networks; Espectrometria y dosimetria de neutrones por medio de redes neuronales evolutivas

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz R, J.M.; Martinez B, M.R.; Vega C, H.R. [UAZ, Av. Ramon Lopez Velarde Num. 801, 98000 Zacatecas (Mexico)

    2008-07-01

    The artificial neural networks and the genetic algorithms are two relatively new areas of research, which have been subject to a growing interest during the last years. Both models are inspired by the nature, however, the neural networks are interested in the learning of a single individual, which is defined as fenotypic learning, while the evolutionary algorithms are interested in the adaptation of a population to a changing environment, that which is defined as genotypic learning. Recently, the use of the technology of neural networks has been applied with success in the area of the nuclear sciences, mainly in the areas of neutron spectrometry and dosimetry. The structure (network topology), as well as the learning parameters of a neural network, are factors that contribute in a significant way with the acting of the same one, however, it has been observed that the investigators in this area, carry out the selection of the network parameters through the essay and error technique, that which produces neural networks of poor performance and low generalization capacity. From the revised sources, it has been observed that the use of the evolutionary algorithms, seen as search techniques, it has allowed him to be possible to evolve and to optimize different properties of the neural networks, just as the initialization of the synaptic weights, the network architecture or the training algorithms without the human intervention. The objective of the present work is focused in analyzing the intersection of the neural networks and the evolutionary algorithms, analyzing like it is that the same ones can be used to help in the design processes and training of a neural network, this is, in the good selection of the structural parameters and of network learning, improving its generalization capacity, in such way that the same one is able to reconstruct in an efficient way neutron spectra and to calculate equivalent doses starting from the counting rates of a Bonner sphere

  10. Dosimetry methods

    DEFF Research Database (Denmark)

    McLaughlin, W.L.; Miller, A.; Kovacs, A.

    2003-01-01

    Chemical and physical radiation dosimetry methods, used for the measurement of absorbed dose mainly during the practical use of ionizing radiation, are discussed with respect to their characteristics and fields of application....

  11. Training of reverse propagation neural networks applied to neutron dosimetry; Entrenamiento de redes neuronales de propagacion inversa aplicadas a la dosimetria de neutrones

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez P, C. F.; Martinez B, M. R.; Leon P, A. A.; Espinoza G, J. G.; Castaneda M, V. H.; Solis S, L. O.; Castaneda M, R.; Ortiz R, M.; Vega C, H. R. [Universidad Autonoma de Zacatecas, Av. Ramon Lopez Velarde 801, Col. Centro, 98000 Zacatecas, Zac. (Mexico); Mendez V, R. [Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas, Laboratorio de Patrones Neutronicos, Av. Complutense 22, 28040 Madrid (Spain); Gallego, E. [Universidad Politecnica de Madrid, Departamento de Ingenieria Nuclear, ETSI Industriales, Jose Gutierrez Abascal 2, 28006 Madrid (Spain); De Sousa L, M. A. [Centro de Desenvolvimento da Tecnologia Nuclear / CNEN, Av. Pte. Antonio Carlos 6627, 31270-901 Pampulha, Belo Horizonte, Minas Gerais (Brazil)

    2016-10-15

    Neutron dosimetry is of great importance in radiation protection as aims to provide dosimetric quantities to assess the magnitude of detrimental health effects due to exposure of neutron radiation. To quantify detriment to health is necessary to evaluate the dose received by the occupationally exposed personnel using different detection systems called dosimeters, which have very dependent responses to the energy distribution of neutrons. The neutron detection is a much more complex problem than the detection of charged particles, since it does not carry an electric charge, does not cause direct ionization and has a greater penetration power giving the possibility of interacting with matter in a different way. Because of this, various neutron detection systems have been developed, among which the Bonner spheres spectrometric system stands out due to the advantages that possesses, such as a wide range of energy, high sensitivity and easy operation. However, once obtained the counting rates, the problem lies in the neutron spectrum deconvolution, necessary for the calculation of the doses, using different mathematical methods such as Monte Carlo, maximum entropy, iterative methods among others, which present various difficulties that have motivated the development of new technologies. Nowadays, methods based on artificial intelligence technologies are being used to perform neutron dosimetry, mainly using the theory of artificial neural networks. In these new methods the need for spectrum reconstruction can be eliminated for the calculation of the doses. In this work an artificial neural network or reverse propagation was trained for the calculation of 15 equivalent doses from the counting rates of the Bonner spheres spectrometric system using a set of 7 spheres, one of 2 spheres and two of a single sphere of different sizes, testing different error values until finding the most appropriate. The optimum network topology was obtained through the robust design

  12. AN EXACT GOODNESS-OF-FIT TEST BASED ON THE OCCUPANCY PROBLEMS TO STUDY ZERO-INFLATION AND ZERO-DEFLATION IN BIOLOGICAL DOSIMETRY DATA.

    Science.gov (United States)

    Fernández-Fontelo, Amanda; Puig, Pedro; Ainsbury, Elizabeth A; Higueras, Manuel

    2018-01-12

    The goal in biological dosimetry is to estimate the dose of radiation that a suspected irradiated individual has received. For that, the analysis of aberrations (most commonly dicentric chromosome aberrations) in scored cells is performed and dose response calibration curves are built. In whole body irradiation (WBI) with X- and gamma-rays, the number of aberrations in samples is properly described by the Poisson distribution, although in partial body irradiation (PBI) the excess of zeros provided by the non-irradiated cells leads, for instance, to the Zero-Inflated Poisson distribution. Different methods are used to analyse the dosimetry data taking into account the distribution of the sample. In order to test the Poisson distribution against the Zero-Inflated Poisson distribution, several asymptotic and exact methods have been proposed which are focused on the dispersion of the data. In this work, we suggest an exact test for the Poisson distribution focused on the zero-inflation of the data developed by Rao and Chakravarti (Some small sample tests of significance for a Poisson distribution. Biometrics 1956; 12 : 264-82.), derived from the problems of occupancy. An approximation based on the standard Normal distribution is proposed in those cases where the computation of the exact test can be tedious. A Monte Carlo Simulation study was performed in order to estimate empirical confidence levels and powers of the exact test and other tests proposed in the literature. Different examples of applications based on in vitro data and also data recorded in several radiation accidents are presented and discussed. A Shiny application which computes the exact test and other interesting goodness-of-fit tests for the Poisson distribution is presented in order to provide them to all interested researchers. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

    Science.gov (United States)

    Li, Jun; Zhao, Patrick X

    2016-01-01

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

  14. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    Anon.

    1981-01-01

    Radiation dosimetry and radiation biophysics are two closely integrated programs whose joint purpose is to explore the connections between the primary physical events produced by radiation and their biological consequences in cellular systems. The radiation dosimetry program includes the theoretical description of primary events and their connection with the observable biological effects. This program also is concerned with the design and measurement of physical parameters used in theory or to support biological experiments. The radiation biophysics program tests and uses the theoretical developments for experimental design, and provides information for further theoretical development through experiments on cellular systems

  15. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    Radiation dosimetry and radiation biophysics are two closely integrated programs whose joint purpose is to explore the connections between the primary physical events produced by radiation and their biological consequences in cellular systems. The radiation dosimetry program includes the theoretical description of primary events and their connection with the observable biological effects. This program also is concerned with design and measurement of those physical parameters used in the theory or to support biological experiments. The radiation biophysics program tests and makes use of the theoretical developments for experimental design. Also, this program provides information for further theoretical development through experiments on cellular systems

  16. CellNet: network biology applied to stem cell engineering.

    Science.gov (United States)

    Cahan, Patrick; Li, Hu; Morris, Samantha A; Lummertz da Rocha, Edroaldo; Daley, George Q; Collins, James J

    2014-08-14

    Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Biologically based neural network for mobile robot navigation

    Science.gov (United States)

    Torres Muniz, Raul E.

    1999-01-01

    The new tendency in mobile robots is to crete non-Cartesian system based on reactions to their environment. This emerging technology is known as Evolutionary Robotics, which is combined with the Biorobotic field. This new approach brings cost-effective solutions, flexibility, robustness, and dynamism into the design of mobile robots. It also provides fast reactions to the sensory inputs, and new interpretation of the environment or surroundings of the mobile robot. The Subsumption Architecture (SA) and the action selection dynamics developed by Brooks and Maes, respectively, have successfully obtained autonomous mobile robots initiating this new trend of the Evolutionary Robotics. Their design keeps the mobile robot control simple. This work present a biologically inspired modification of these schemes. The hippocampal-CA3-based neural network developed by Williams Levy is used to implement the SA, while the action selection dynamics emerge from iterations of the levels of competence implemented with the HCA3. This replacement by the HCA3 results in a closer biological model than the SA, combining the Behavior-based intelligence theory with neuroscience. The design is kept simple, and it is implemented in the Khepera Miniature Mobile Robot. The used control scheme obtains an autonomous mobile robot that can be used to execute a mail delivery system and surveillance task inside a building floor.

  18. Multilayer network modeling creates opportunities for novel network statistics. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

    Science.gov (United States)

    Muldoon, Sarah Feldt

    2018-03-01

    As described in the review by Gosak et al., the field of network science has had enormous success in providing new insights into the structure and function of biological systems [1]. In the complex networks framework, system elements are network nodes, and connections between nodes represent some form of interaction between system elements [2]. The flexibility to define network nodes and edges to represent different aspects of biological systems has been employed to model numerous diverse systems at multiple scales.

  19. Techniques for radiation measurements: Micro-dosimetry and dosimetry

    International Nuclear Information System (INIS)

    Waker, A. J.

    2006-01-01

    Experimental Micro-dosimetry is concerned with the determination of radiation quality and how this can be specified in terms of the distribution of energy deposition arising from the interaction of a radiation field with a particular target site. This paper discusses various techniques that have been developed to measure radiation energy deposition over the three orders of magnitude of site-size; nano-meter, micrometer and millimetre, which radiation biology suggests is required to fully account for radiation quality. Inevitably, much of the discussion will concern the use of tissue-equivalent proportional counters and variants of this device, but other technologies that have been studied, or are under development, for their potential in experimental Micro-dosimetry are also covered. Through an examination of some of the quantities used in radiation metrology and dosimetry the natural link with Micro-dosimetric techniques will be shown and the particular benefits of using Micro-dosimetric methods for dosimetry illustrated. (authors)

  20. Exposure to mobile telecommunication networks assessed using personal dosimetry and well-being in children and adolescents: the German MobilEe-study.

    Science.gov (United States)

    Thomas, Silke; Kühnlein, Anja; Heinrich, Sabine; Praml, Georg; von Kries, Rüdiger; Radon, Katja

    2008-11-04

    Despite the increase of mobile phone use in the last decade and the growing concern whether mobile telecommunication networks adversely affect health and well-being, only few studies have been published that focussed on children and adolescents. Especially children and adolescents are important in the discussion of adverse health effects because of their possibly higher vulnerability to radio frequency electromagnetic fields. We investigated a possible association between exposure to mobile telecommunication networks and well-being in children and adolescents using personal dosimetry. A population-based sample of 1.498 children and 1.524 adolescents was assembled for the study (response 52%). Participants were randomly selected from the population registries of four Bavarian (South of Germany) cities and towns with different population sizes. During a Computer Assisted Personal Interview data on participants' well-being, socio-demographic characteristics and potential confounder were collected. Acute symptoms were assessed three times during the study day (morning, noon, evening).Using a dosimeter (ESM-140 Maschek Electronics), we obtained an exposure profile over 24 hours for three mobile phone frequency ranges (measurement interval 1 second, limit of determination 0.05 V/m) for each of the participants. Exposure levels over waking hours were summed up and expressed as mean percentage of the ICNIRP (International Commission on Non-Ionizing Radiation Protection) reference level. In comparison to non-participants, parents and adolescents with a higher level of education who possessed a mobile phone and were interested in the topic of possible adverse health effects caused by mobile telecommunication network frequencies were more willing to participate in the study. The median exposure to radio frequency electromagnetic fields of children and adolescents was 0.18% and 0.19% of the ICNIRP reference level respectively. In comparison to previous studies this is one of

  1. Exposure to mobile telecommunication networks assessed using personal dosimetry and well-being in children and adolescents: the German MobilEe-study

    Directory of Open Access Journals (Sweden)

    von Kries Rüdiger

    2008-11-01

    Full Text Available Abstract Background Despite the increase of mobile phone use in the last decade and the growing concern whether mobile telecommunication networks adversely affect health and well-being, only few studies have been published that focussed on children and adolescents. Especially children and adolescents are important in the discussion of adverse health effects because of their possibly higher vulnerability to radio frequency electromagnetic fields. Methods We investigated a possible association between exposure to mobile telecommunication networks and well-being in children and adolescents using personal dosimetry. A population-based sample of 1.498 children and 1.524 adolescents was assembled for the study (response 52%. Participants were randomly selected from the population registries of four Bavarian (South of Germany cities and towns with different population sizes. During a Computer Assisted Personal Interview data on participants' well-being, socio-demographic characteristics and potential confounder were collected. Acute symptoms were assessed three times during the study day (morning, noon, evening. Using a dosimeter (ESM-140 Maschek Electronics, we obtained an exposure profile over 24 hours for three mobile phone frequency ranges (measurement interval 1 second, limit of determination 0.05 V/m for each of the participants. Exposure levels over waking hours were summed up and expressed as mean percentage of the ICNIRP (International Commission on Non-Ionizing Radiation Protection reference level. Results In comparison to non-participants, parents and adolescents with a higher level of education who possessed a mobile phone and were interested in the topic of possible adverse health effects caused by mobile telecommunication network frequencies were more willing to participate in the study. The median exposure to radio frequency electromagnetic fields of children and adolescents was 0.18% and 0.19% of the ICNIRP reference level respectively

  2. Dosimetry in life sciences

    International Nuclear Information System (INIS)

    1975-01-01

    The uses of radiation in medicine and biology have grown in scope and diversity to make the Radiological Sciences a significant factor in both research and medical practice. Of critical importance in the applications and development of biomedical and radiological techniques is the precision with which the dose may be determined at all points of interest in the absorbing medium. This has developed as a result of efficacy of investigations in clinical radiation therapy, concern for patient safety and diagnostic accuracy in diagnostic radiology and the advent of clinical trials and research into the use of heavily ionizing radiations in biology and medicine. Since the last IAEA Symposium on Dosimetry Techniques applied to Agriculture, Industry, Biology and Medicine, held in Vienna in 1972, it has become increasingly clear that advances in the techniques and hardware of biomedical dosimetry have been rapid. It is for these reasons that this symposium was organized in a concerted effort to focus on the problems, developments and areas of further research in dosimetry in the Life Sciences. (author)

  3. Dosimetry in life sciences

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1975-06-15

    The uses of radiation in medicine and biology have grown in scope and diversity to make the Radiological Sciences a significant factor in both research and medical practice. Of critical importance in the applications and development of biomedical and radiological techniques is the precision with which the dose may be determined at all points of interest in the absorbing medium. This has developed as a result of efficacy of investigations in clinical radiation therapy, concern for patient safety and diagnostic accuracy in diagnostic radiology and the advent of clinical trials and research into the use of heavily ionizing radiations in biology and medicine. Since the last IAEA Symposium on Dosimetry Techniques applied to Agriculture, Industry, Biology and Medicine, held in Vienna in 1972, it has become increasingly clear that advances in the techniques and hardware of biomedical dosimetry have been rapid. It is for these reasons that this symposium was organized in a concerted effort to focus on the problems, developments and areas of further research in dosimetry in the Life Sciences. (author)

  4. Network Biology (http://www.iaees.org/publications/journals/nb/online-version.asp

    Directory of Open Access Journals (Sweden)

    networkbiology@iaees.org

    Full Text Available Network Biology ISSN 2220-8879 URL: http://www.iaees.org/publications/journals/nb/online-version.asp RSS: http://www.iaees.org/publications/journals/nb/rss.xml E-mail: networkbiology@iaees.org Editor-in-Chief: WenJun Zhang Aims and Scope NETWORK BIOLOGY (ISSN 2220-8879; CODEN NBEICS is an open access, peer-reviewed international journal that considers scientific articles in all different areas of network biology. It is the transactions of the International Society of Network Biology. It dedicates to the latest advances in network biology. The goal of this journal is to keep a record of the state-of-the-art research and promote the research work in these fast moving areas. The topics to be covered by Network Biology include, but are not limited to: •Theories, algorithms and programs of network analysis •Innovations and applications of biological networks •Ecological networks, food webs and natural equilibrium •Co-evolution, co-extinction, biodiversity conservation •Metabolic networks, protein-protein interaction networks, biochemical reaction networks, gene networks, transcriptional regulatory networks, cell cycle networks, phylogenetic networks, network motifs •Physiological networksNetwork regulation of metabolic processes, human diseases and ecological systems •Social networks, epidemiological networks •System complexity, self-organized systems, emergence of biological systems, agent-based modeling, individual-based modeling, neural network modeling, and other network-based modeling, etc. We are also interested in short communications that clearly address a specific issue or completely present a new ecological network, food web, or metabolic or gene network, etc. Authors can submit their works to the email box of this journal, networkbiology@iaees.org. All manuscripts submitted to this journal must be previously unpublished and may not be considered for publication elsewhere at any time during review period of this journal

  5. Clinical dosimetry

    International Nuclear Information System (INIS)

    Rassow, J.

    1973-01-01

    The main point of this paper on clinical dosimetry which is to be understood here as application of physical dosimetry on accelerators in medical practice, is based on dosimetric methodics. Following an explanation of the dose parameters and description of the dose distribution important for clinical practice as well as geometric irradiation parameters, the significance of a series of physical parameters such as accelerator energy, surface energy of average stopping power etc. is dealt with in detail. Following a section on field homogenization with bremsstrahlung and electron radiation, details on dosimetry in clinical practice are given. Finally, a few problems of dosemeter or monitor calibration on accelerators are described. The explanations are supplemented by a series of diagrams and tables. (ORU/LH) [de

  6. An efficient grid layout algorithm for biological networks utilizing various biological attributes

    Directory of Open Access Journals (Sweden)

    Kato Mitsuru

    2007-03-01

    Full Text Available Abstract Background Clearly visualized biopathways provide a great help in understanding biological systems. However, manual drawing of large-scale biopathways is time consuming. We proposed a grid layout algorithm that can handle gene-regulatory networks and signal transduction pathways by considering edge-edge crossing, node-edge crossing, distance measure between nodes, and subcellular localization information from Gene Ontology. Consequently, the layout algorithm succeeded in drastically reducing these crossings in the apoptosis model. However, for larger-scale networks, we encountered three problems: (i the initial layout is often very far from any local optimum because nodes are initially placed at random, (ii from a biological viewpoint, human layouts still exceed automatic layouts in understanding because except subcellular localization, it does not fully utilize biological information of pathways, and (iii it employs a local search strategy in which the neighborhood is obtained by moving one node at each step, and automatic layouts suggest that simultaneous movements of multiple nodes are necessary for better layouts, while such extension may face worsening the time complexity. Results We propose a new grid layout algorithm. To address problem (i, we devised a new force-directed algorithm whose output is suitable as the initial layout. For (ii, we considered that an appropriate alignment of nodes having the same biological attribute is one of the most important factors of the comprehension, and we defined a new score function that gives an advantage to such configurations. For solving problem (iii, we developed a search strategy that considers swapping nodes as well as moving a node, while keeping the order of the time complexity. Though a naïve implementation increases by one order, the time complexity, we solved this difficulty by devising a method that caches differences between scores of a layout and its possible updates

  7. Assessment of radiation damage - the need for a multi-parametric and integrative approach with the help of both clinical and biological dosimetry

    International Nuclear Information System (INIS)

    Meineke, Viktor

    2008-01-01

    Full text: Accidental exposure to ionising radiation leads to a damage on different levels of the biological organization of the organism. Depending on exposure conditions, such as nature of radiation, time and affected organs and organ systems, the clinical endpoint of radiation damage and the resulting acute and chronic radiation syndromes may vary to a great extent. Exposure situations range from pure localised radiation scenarios and partial body exposures up to whole body exposures. Therefore clinical pictures vary from localized radiation injuries up to the extreme situation of a radiation-induced multi-organ involvement and failure requiring immediate, intensive and interdisciplinary medical treatment. These total different and complex clinical situations not only show up most different clinical diagnostic and therapeutic aspects but necessarily due to different levels of the underlying biological damage, biological indicators of effects may vary to a wide extent. This fact means that an exact assessment of the extent of radiation damage within individual patients can only be performed when taking into consideration both clinical signs and symptoms as well as different biological indicators. Among the clinical indicators, routine laboratory parameters such as blood counts and the documentation of clinical signs and symptoms (such as the METREPOL system) are the key parameters, whereas the dicentric assay, the gold standard for biological dosimetry, but also methods under development such as the gamma-H2Ax focus assay or the estimation of variations of gene expression have to be taken into account. Each method provides best results in different situations, or in other words, there are methods that work better in a specific exposure condition or at a given time of examination (e.g. time after exposure) than others. Some methods show up results immediately, others require days to weeks until results are available for clinical decision making. Therefore to

  8. Novel recurrent neural network for modelling biological networks: oscillatory p53 interaction dynamics.

    Science.gov (United States)

    Ling, Hong; Samarasinghe, Sandhya; Kulasiri, Don

    2013-12-01

    Understanding the control of cellular networks consisting of gene and protein interactions and their emergent properties is a central activity of Systems Biology research. For this, continuous, discrete, hybrid, and stochastic methods have been proposed. Currently, the most common approach to modelling accurate temporal dynamics of networks is ordinary differential equations (ODE). However, critical limitations of ODE models are difficulty in kinetic parameter estimation and numerical solution of a large number of equations, making them more suited to smaller systems. In this article, we introduce a novel recurrent artificial neural network (RNN) that addresses above limitations and produces a continuous model that easily estimates parameters from data, can handle a large number of molecular interactions and quantifies temporal dynamics and emergent systems properties. This RNN is based on a system of ODEs representing molecular interactions in a signalling network. Each neuron represents concentration change of one molecule represented by an ODE. Weights of the RNN correspond to kinetic parameters in the system and can be adjusted incrementally during network training. The method is applied to the p53-Mdm2 oscillation system - a crucial component of the DNA damage response pathways activated by a damage signal. Simulation results indicate that the proposed RNN can successfully represent the behaviour of the p53-Mdm2 oscillation system and solve the parameter estimation problem with high accuracy. Furthermore, we presented a modified form of the RNN that estimates parameters and captures systems dynamics from sparse data collected over relatively large time steps. We also investigate the robustness of the p53-Mdm2 system using the trained RNN under various levels of parameter perturbation to gain a greater understanding of the control of the p53-Mdm2 system. Its outcomes on robustness are consistent with the current biological knowledge of this system. As more

  9. Complex network problems in physics, computer science and biology

    Science.gov (United States)

    Cojocaru, Radu Ionut

    There is a close relation between physics and mathematics and the exchange of ideas between these two sciences are well established. However until few years ago there was no such a close relation between physics and computer science. Even more, only recently biologists started to use methods and tools from statistical physics in order to study the behavior of complex system. In this thesis we concentrate on applying and analyzing several methods borrowed from computer science to biology and also we use methods from statistical physics in solving hard problems from computer science. In recent years physicists have been interested in studying the behavior of complex networks. Physics is an experimental science in which theoretical predictions are compared to experiments. In this definition, the term prediction plays a very important role: although the system is complex, it is still possible to get predictions for its behavior, but these predictions are of a probabilistic nature. Spin glasses, lattice gases or the Potts model are a few examples of complex systems in physics. Spin glasses and many frustrated antiferromagnets map exactly to computer science problems in the NP-hard class defined in Chapter 1. In Chapter 1 we discuss a common result from artificial intelligence (AI) which shows that there are some problems which are NP-complete, with the implication that these problems are difficult to solve. We introduce a few well known hard problems from computer science (Satisfiability, Coloring, Vertex Cover together with Maximum Independent Set and Number Partitioning) and then discuss their mapping to problems from physics. In Chapter 2 we provide a short review of combinatorial optimization algorithms and their applications to ground state problems in disordered systems. We discuss the cavity method initially developed for studying the Sherrington-Kirkpatrick model of spin glasses. We extend this model to the study of a specific case of spin glass on the Bethe

  10. Biological mechanisms beyond network analysis via mathematical modeling. Comment on "Network science of biological systems at different scales: A review" by Marko Gosak et al.

    Science.gov (United States)

    Pedersen, Morten Gram

    2018-03-01

    Methods from network theory are increasingly used in research spanning from engineering and computer science to psychology and the social sciences. In this issue, Gosak et al. [1] provide a thorough review of network science applications to biological systems ranging from the subcellular world via neuroscience to ecosystems, with special attention to the insulin-secreting beta-cells in pancreatic islets.

  11. Neural network models for biological waste-gas treatment systems.

    Science.gov (United States)

    Rene, Eldon R; Estefanía López, M; Veiga, María C; Kennes, Christian

    2011-12-15

    This paper outlines the procedure for developing artificial neural network (ANN) based models for three bioreactor configurations used for waste-gas treatment. The three bioreactor configurations chosen for this modelling work were: biofilter (BF), continuous stirred tank bioreactor (CSTB) and monolith bioreactor (MB). Using styrene as the model pollutant, this paper also serves as a general database of information pertaining to the bioreactor operation and important factors affecting gas-phase styrene removal in these biological systems. Biological waste-gas treatment systems are considered to be both advantageous and economically effective in treating a stream of polluted air containing low to moderate concentrations of the target contaminant, over a rather wide range of gas-flow rates. The bioreactors were inoculated with the fungus Sporothrix variecibatus, and their performances were evaluated at different empty bed residence times (EBRT), and at different inlet styrene concentrations (C(i)). The experimental data from these bioreactors were modelled to predict the bioreactors performance in terms of their removal efficiency (RE, %), by adequate training and testing of a three-layered back propagation neural network (input layer-hidden layer-output layer). Two models (BIOF1 and BIOF2) were developed for the BF with different combinations of easily measurable BF parameters as the inputs, that is concentration (gm(-3)), unit flow (h(-1)) and pressure drop (cm of H(2)O). The model developed for the CSTB used two inputs (concentration and unit flow), while the model for the MB had three inputs (concentration, G/L (gas/liquid) ratio, and pressure drop). Sensitivity analysis in the form of absolute average sensitivity (AAS) was performed for all the developed ANN models to ascertain the importance of the different input parameters, and to assess their direct effect on the bioreactors performance. The performance of the models was estimated by the regression

  12. The redox biology network in cancer pathophysiology and therapeutics

    Directory of Open Access Journals (Sweden)

    Gina Manda

    2015-08-01

    Full Text Available The review pinpoints operational concepts related to the redox biology network applied to the pathophysiology and therapeutics of solid tumors. A sophisticated network of intrinsic and extrinsic cues, integrated in the tumor niche, drives tumorigenesis and tumor progression. Critical mutations and distorted redox signaling pathways orchestrate pathologic events inside cancer cells, resulting in resistance to stress and death signals, aberrant proliferation and efficient repair mechanisms. Additionally, the complex inter-cellular crosstalk within the tumor niche, mediated by cytokines, redox-sensitive danger signals (HMGB1 and exosomes, under the pressure of multiple stresses (oxidative, inflammatory, metabolic, greatly contributes to the malignant phenotype. The tumor-associated inflammatory stress and its suppressive action on the anti-tumor immune response are highlighted. We further emphasize that ROS may act either as supporter or enemy of cancer cells, depending on the context. Oxidative stress-based therapies, such as radiotherapy and photodynamic therapy, take advantage of the cytotoxic face of ROS for killing tumor cells by a non-physiologically sudden, localized and intense oxidative burst. The type of tumor cell death elicited by these therapies is discussed. Therapy outcome depends on the differential sensitivity to oxidative stress of particular tumor cells, such as cancer stem cells, and therefore co-therapies that transiently down-regulate their intrinsic antioxidant system hold great promise. We draw attention on the consequences of the damage signals delivered by oxidative stress-injured cells to neighboring and distant cells, and emphasize the benefits of therapeutically triggered immunologic cell death in metastatic cancer. An integrative approach should be applied when designing therapeutic strategies in cancer, taking into consideration the mutational, metabolic, inflammatory and oxidative status of tumor cells, cellular

  13. Biological dosimetry - a Bayesian approach in the presentation of the uncertainty of the estimated dose in cases of exposure to low dose radiation

    International Nuclear Information System (INIS)

    Di Giorgio, Marina; Zaretzky, A.

    2010-01-01

    Biodosimetry laboratory experience has shown that there are limitations in the existing statistical methodology. Statistical difficulties generally occur due to the low number of aberrations leading to large uncertainties for dose estimation. Some problems derived from limitations of the classical statistical methodology, which requires that chromosome aberration yields be considered as something fixed and consequently provides a deterministic dose estimation and associated confidence limits. On the other hand, recipients of biological dosimetry reports, including medical doctors, regulators and the patients themselves may have a limited comprehension of statistics and of informed reports. Thus, the objective of the present paper is to use a Bayesian approach to present the uncertainty on the estimated dose to which a person could be exposed, in the case of low dose (occupational doses) radiation exposure. Such methodology will allow the biodosimetrists to adopt a probabilistic approach for the cytogenetic data analysis. At present, classical statistics allows to produce a confidence interval to report such dose, with a lower limit that could not detach from zero. In this situation it becomes difficult to make decisions as they could impact on the labor activities of the worker if an exposure exceeding the occupational dose limits is inferred. The proposed Bayesian approach is applied to occupational exposure scenario to contribute to take the appropriate radiation protection measures. (authors) [es

  14. Environmental dosimetry

    International Nuclear Information System (INIS)

    Gold, R.

    1977-01-01

    For more than 60 years, natural radiation has offered broad opportunities for basic research as evidenced by many fundamental discoveries. Within the last decade, however, dramatic changes have occurred in the motivation and direction of this research. The urgent need for economical energy sources entailing acceptably low levels of environmental impact has compelled the applied aspects of our radiation environment to become overriding considerations. It is within this general framework that state-of-the-art environmental dosimetry techniques are reviewed. Although applied motivation and relevance underscores the current milieu for both reactor and environmental dosimetry, a perhaps even more unifying force is the broad similarity of reactor and environmental radiation fields. In this review, a comparison of these two mixed radiation fields is presented stressing the underlying similarities that exist. On this basis, the evolution of a strong inner bond between dosimetry methods for both reactor and environmental radiation fields is described. The existence of this bond will be illustrated using representative examples of observed spectra. Dosimetry methods of particularly high applicability for both of these fields are described. Special emphasis is placed on techniques of high sensitivity and absolute accuracy which are capable of resolving the components of these mixed radiation fields

  15. Quantitative autoradiography of radionuclides in biological tissues by high resolution nuclear analysis: application in radio-toxicology and dosimetry

    International Nuclear Information System (INIS)

    Aubineau Laniece, I.

    1997-01-01

    In the framework of radiation damage on cells in living organisms an auto-radiograph, based on the STIC method, has been developed for the particles detection. This apparatus associates a thin scintillator with a photosensitive detector (CCD). The design and the performance of this well adapted tool for low activity biological samples study, are described. (A.L.B.)

  16. Elucidation of time-dependent systems biology cell response patterns with time course network enrichment

    DEFF Research Database (Denmark)

    Wiwie, Christian; Rauch, Alexander; Haakonsson, Anders

    2018-01-01

    , no methods exist to integrate time series data with networks, thus preventing the identification of time-dependent systems biology responses. We close this gap with Time Course Network Enrichment (TiCoNE). It combines a new kind of human-augmented clustering with a novel approach to network enrichment...

  17. A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology

    Science.gov (United States)

    Chen, Bor-Sen; Lin, Ying-Po

    2013-01-01

    Robust stabilization and environmental disturbance attenuation are ubiquitous systematic properties that are observed in biological systems at many different levels. The underlying principles for robust stabilization and environmental disturbance attenuation are universal to both complex biological systems and sophisticated engineering systems. In many biological networks, network robustness should be large enough to confer: intrinsic robustness for tolerating intrinsic parameter fluctuations; genetic robustness for buffering genetic variations; and environmental robustness for resisting environmental disturbances. Network robustness is needed so phenotype stability of biological network can be maintained, guaranteeing phenotype robustness. Synthetic biology is foreseen to have important applications in biotechnology and medicine; it is expected to contribute significantly to a better understanding of functioning of complex biological systems. This paper presents a unifying mathematical framework for investigating the principles of both robust stabilization and environmental disturbance attenuation for synthetic gene networks in synthetic biology. Further, from the unifying mathematical framework, we found that the phenotype robustness criterion for synthetic gene networks is the following: if intrinsic robustness + genetic robustness + environmental robustness ≦ network robustness, then the phenotype robustness can be maintained in spite of intrinsic parameter fluctuations, genetic variations, and environmental disturbances. Therefore, the trade-offs between intrinsic robustness, genetic robustness, environmental robustness, and network robustness in synthetic biology can also be investigated through corresponding phenotype robustness criteria from the systematic point of view. Finally, a robust synthetic design that involves network evolution algorithms with desired behavior under intrinsic parameter fluctuations, genetic variations, and environmental

  18. KeyPathwayMiner - De-novo network enrichment by combining multiple OMICS data and biological networks

    DEFF Research Database (Denmark)

    Baumbach, Jan; Alcaraz, Nicolas; Pauling, Josch K.

    We tackle the problem of de-novo pathway extraction. Given a biological network and a set of case-control studies, KeyPathwayMiner efficiently extracts and visualizes all maximal connected sub-networks that contain mainly genes that are dysregulated, e.g., differentially expressed, in most cases ...

  19. Neutron personnel dosimetry

    International Nuclear Information System (INIS)

    Griffith, R.V.

    1981-01-01

    The current state-of-the-art in neutron personnel dosimetry is reviewed. Topics covered include dosimetry needs and alternatives, current dosimetry approaches, personnel monitoring devices, calibration strategies, and future developments

  20. Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks

    Science.gov (United States)

    2018-01-01

    Signaling pathways represent parts of the global biological molecular network which connects them into a seamless whole through complex direct and indirect (hidden) crosstalk whose structure can change during development or in pathological conditions. We suggest a novel methodology, called Googlomics, for the structural analysis of directed biological networks using spectral analysis of their Google matrices, using parallels with quantum scattering theory, developed for nuclear and mesoscopic physics and quantum chaos. We introduce analytical “reduced Google matrix” method for the analysis of biological network structure. The method allows inferring hidden causal relations between the members of a signaling pathway or a functionally related group of genes. We investigate how the structure of hidden causal relations can be reprogrammed as a result of changes in the transcriptional network layer during cancerogenesis. The suggested Googlomics approach rigorously characterizes complex systemic changes in the wiring of large causal biological networks in a computationally efficient way. PMID:29370181

  1. Biological dosimetry to determine the UV radiation climate inside the MIR station and its role in vitamin D biosynthesis

    Science.gov (United States)

    Rettberg, P.; Horneck, G.; Zittermann, A.; Heer, M.

    1998-11-01

    The vitamin D synthesis in the human skin, is absolutely dependent on UVB radiation. Natural UVB from sunlight is normally absent in the closed environment of a space station like MIR. Therefore it was necessary to investigate the UV radiation climate inside the station resulting from different lamps as well as from occasional solar irradiation behind a UV-transparent quartz window. Biofilms, biologically weighting and integrating UV dosimeters successfully applied on Earth (e.g. in Antarctica) and in space (D-2, Biopan I) were used to determine the biological effectiveness of the UV radiation climate at different locations in the space station. Biofilms were also used to determine the personal UV dose of an individual cosmonaut. These UV data were correlated with the concentration of vitamin D in the cosmonaut's blood and the dietary vitamin D intake. The results showed that the UV radiation climate inside the Mir station is not sufficient for an adequate supply of vitamin D, which should therefore be secured either by vitamin D supplementat and/or by the regular exposure to special UV lamps like those in sun-beds. The use of natural solar UV radiation through the quartz window for `sunbathing' is dangerous and should be avoided even for short exposure periods.

  2. Integration of biological networks and gene expression data using Cytoscape

    DEFF Research Database (Denmark)

    Cline, M.S.; Smoot, M.; Cerami, E.

    2007-01-01

    of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules......Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context...... and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape....

  3. Hematological dosimetry

    International Nuclear Information System (INIS)

    Fluery-Herard, A.

    1991-01-01

    The principles of hematological dosimetry after acute or protracted whole-body irradiation are reviewed. In both cases, over-exposure is never homogeneous and the clinical consequences, viz medullary aplasia, are directly associated with the mean absorbed dose and the seriousness and location of the overexposure. The main hematological data required to assess the seriousness of exposure are the following: repeated blood analysis, blood precursor cultures, as indicators of whole-body exposure; bone marrow puncture, medullary precursor cultures and medullary scintigraphy as indicators of the importance of a local over-exposure and capacity for spontaneous repair. These paraclinical investigations, which are essential for diagnosis and dosimetry, are also used for surveillance and for the main therapeutic issues [fr

  4. Dosimetry: an ARDENT topic

    CERN Multimedia

    CERN Bulletin

    2012-01-01

    The first annual ARDENT workshop took place in Vienna from 20 to 23 November. The workshop gathered together the Early-Stage Researchers (ESR) and their supervisors, plus other people involved from all the participating institutions.   “The meeting, which was organised with the local support of the Austrian Institute of Technology, was a nice opportunity for the ESRs to get together, meet each other, and present their research plans and some preliminary results of their work,” says Marco Silari, a member of CERN Radiation Protection Group and the scientist in charge of the programme. Two full days were devoted to a training course on radiation dosimetry, delivered by renowned experts. The workshop closed with a half-day visit to the MedAustron facility in Wiener Neustadt. ARDENT (Advanced Radiation Dosimetry European Network Training) is a Marie Curie ITN project funded under EU FP7 with €4 million. The project focuses on radiation dosimetry exploiting se...

  5. Dosimetry in dentistry.

    Science.gov (United States)

    Asha, M L; Chatterjee, Ingita; Patil, Preeti; Naveen, S

    2015-01-01

    The purpose of this paper was to review various dosimeters used in dentistry and the cumulative results of various studies done with various dosimeters. Several relevant PubMed indexed articles from 1999 to 2013 were electronically searched by typing "dosimeters", "dosimeters in dentistry", "properties of dosimeters", "thermoluminescent and optically stimulated dosimeters", "recent advancements in dosimetry in dentistry." The searches were limited to articles in English to prepare a concise review on dental dosimetry. Titles and abstracts were screened, and articles that fulfilled the criteria of use of dosimeters in dental applications were selected for a full-text reading. Article was divided into four groups: (1) Biological effects of radiation, (2) properties of dosimeters, (3) types of dosimeters and (4) results of various studies using different dosimeters. The present review on dosimetry based on various studies done with dosimeters revealed that, with the advent of radiographic technique the effective dose delivered is low. Therefore, selection of radiological technique plays an important role in dental dose delivery.

  6. Amylase and blood cell-count hematological radiation-injury biomarkers in a rhesus monkey radiation model-use of multiparameter and integrated biological dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Blakely, W.F. [Uniformed Services University, Armed Forces Radiobiology Research Institute, 8901 Wisconsin Avenue, Bethesda, MD 20889-5603 (United States)], E-mail: blakely@afrri.usuhs.mil; Ossetrova, N.I.; Manglapus, G.L.; Salter, C.A.; Levine, I.H.; Jackson, W.E.; Grace, M.B.; Prasanna, P.G.S.; Sandgren, D.J.; Ledney, G.D. [Uniformed Services University, Armed Forces Radiobiology Research Institute, 8901 Wisconsin Avenue, Bethesda, MD 20889-5603 (United States)

    2007-07-15

    Effective medical management of suspected radiation exposure incidents requires the recording of dynamic medical data (clinical signs and symptoms), biological assessments of radiation exposure, and physical dosimetry in order to provide diagnostic information to the treating physician and dose assessment for personnel radiation protection records. The need to rapidly assess radiation dose in mass-casualty and population-monitoring scenarios prompted an evaluation of suitable biomarkers that can provide early diagnostic information after exposure. We investigated the utility of serum amylase and hematological blood-cell count biomarkers to provide early assessment of severe radiation exposures in a non-human primate model (i.e., rhesus macaques; n=8) exposed to whole-body radiation of {sup 60}Co-gamma rays (6.5 Gy, 40cGymin{sup -1}). Serum amylase activity was significantly elevated (12.3{+-}3.27- and 2.6{+-}0.058-fold of day zero samples) at 1 and 2-days, respectively, after radiation. Lymphocyte cell counts decreased ({<=}15% of day zero samples) 1 and 2 days after radiation exposure. Neutrophil cell counts increased at day one by 1.9({+-}0.38)-fold compared with levels before irradiation. The ratios of neutrophil to lymphocyte cell counts increased by 13({+-}2.66)- and 4.23({+-}0.95)-fold at 1 and 2 days, respectively, after irradiation. These results demonstrate that increases in serum amylase activity along with decreases of lymphocyte counts, increases in neutrophil cell counts, and increases in the ratio of neutrophil to lymphocyte counts 1 day after irradiation can provide enhanced early triage discrimination of individuals with severe radiation exposure and injury. Use of the biodosimetry assessment tool (BAT) application is encouraged to permit dynamic recording of medical data in the management of a suspected radiological casualty.

  7. Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

    Directory of Open Access Journals (Sweden)

    Shuo Gu

    2017-01-01

    Full Text Available With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

  8. Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective.

    Science.gov (United States)

    Gu, Shuo; Pei, Jianfeng

    2017-01-01

    With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.

  9. NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.

    Science.gov (United States)

    Theodosiou, Theodosios; Efstathiou, Georgios; Papanikolaou, Nikolas; Kyrpides, Nikos C; Bagos, Pantelis G; Iliopoulos, Ioannis; Pavlopoulos, Georgios A

    2017-07-14

    Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks. Network Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .

  10. Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research.

    Science.gov (United States)

    Jinawath, Natini; Bunbanjerdsuk, Sacarin; Chayanupatkul, Maneerat; Ngamphaiboon, Nuttapong; Asavapanumas, Nithi; Svasti, Jisnuson; Charoensawan, Varodom

    2016-11-22

    With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases.

  11. Robustness of the p53 network and biological hackers.

    Science.gov (United States)

    Dartnell, Lewis; Simeonidis, Evangelos; Hubank, Michael; Tsoka, Sophia; Bogle, I David L; Papageorgiou, Lazaros G

    2005-06-06

    The p53 protein interaction network is crucial in regulating the metazoan cell cycle and apoptosis. Here, the robustness of the p53 network is studied by analyzing its degeneration under two modes of attack. Linear Programming is used to calculate average path lengths among proteins and the network diameter as measures of functionality. The p53 network is found to be robust to random loss of nodes, but vulnerable to a targeted attack against its hubs, as a result of its architecture. The significance of the results is considered with respect to mutational knockouts of proteins and the directed attacks mounted by tumour inducing viruses.

  12. Revisiting the variation of clustering coefficient of biological networks suggests new modular structure.

    Science.gov (United States)

    Hao, Dapeng; Ren, Cong; Li, Chuanxing

    2012-05-01

    A central idea in biology is the hierarchical organization of cellular processes. A commonly used method to identify the hierarchical modular organization of network relies on detecting a global signature known as variation of clustering coefficient (so-called modularity scaling). Although several studies have suggested other possible origins of this signature, it is still widely used nowadays to identify hierarchical modularity, especially in the analysis of biological networks. Therefore, a further and systematical investigation of this signature for different types of biological networks is necessary. We analyzed a variety of biological networks and found that the commonly used signature of hierarchical modularity is actually the reflection of spoke-like topology, suggesting a different view of network architecture. We proved that the existence of super-hubs is the origin that the clustering coefficient of a node follows a particular scaling law with degree k in metabolic networks. To study the modularity of biological networks, we systematically investigated the relationship between repulsion of hubs and variation of clustering coefficient. We provided direct evidences for repulsion between hubs being the underlying origin of the variation of clustering coefficient, and found that for biological networks having no anti-correlation between hubs, such as gene co-expression network, the clustering coefficient doesn't show dependence of degree. Here we have shown that the variation of clustering coefficient is neither sufficient nor exclusive for a network to be hierarchical. Our results suggest the existence of spoke-like modules as opposed to "deterministic model" of hierarchical modularity, and suggest the need to reconsider the organizational principle of biological hierarchy.

  13. Revisiting the variation of clustering coefficient of biological networks suggests new modular structure

    Directory of Open Access Journals (Sweden)

    Hao Dapeng

    2012-05-01

    Full Text Available Abstract Background A central idea in biology is the hierarchical organization of cellular processes. A commonly used method to identify the hierarchical modular organization of network relies on detecting a global signature known as variation of clustering coefficient (so-called modularity scaling. Although several studies have suggested other possible origins of this signature, it is still widely used nowadays to identify hierarchical modularity, especially in the analysis of biological networks. Therefore, a further and systematical investigation of this signature for different types of biological networks is necessary. Results We analyzed a variety of biological networks and found that the commonly used signature of hierarchical modularity is actually the reflection of spoke-like topology, suggesting a different view of network architecture. We proved that the existence of super-hubs is the origin that the clustering coefficient of a node follows a particular scaling law with degree k in metabolic networks. To study the modularity of biological networks, we systematically investigated the relationship between repulsion of hubs and variation of clustering coefficient. We provided direct evidences for repulsion between hubs being the underlying origin of the variation of clustering coefficient, and found that for biological networks having no anti-correlation between hubs, such as gene co-expression network, the clustering coefficient doesn’t show dependence of degree. Conclusions Here we have shown that the variation of clustering coefficient is neither sufficient nor exclusive for a network to be hierarchical. Our results suggest the existence of spoke-like modules as opposed to “deterministic model” of hierarchical modularity, and suggest the need to reconsider the organizational principle of biological hierarchy.

  14. CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

    Science.gov (United States)

    Li, Min; Li, Dongyan; Tang, Yu; Wu, Fangxiang; Wang, Jianxin

    2017-08-31

    Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.

  15. Social network size relates to developmental neural sensitivity to biological motion

    Directory of Open Access Journals (Sweden)

    L.A. Kirby

    2018-04-01

    Full Text Available The ability to perceive others’ actions and goals from human motion (i.e., biological motion perception is a critical component of social perception and may be linked to the development of real-world social relationships. Adult research demonstrates two key nodes of the brain’s biological motion perception system—amygdala and posterior superior temporal sulcus (pSTS—are linked to variability in social network properties. The relation between social perception and social network properties, however, has not yet been investigated in middle childhood—a time when individual differences in social experiences and social perception are growing. The aims of this study were to (1 replicate past work showing amygdala and pSTS sensitivity to biological motion in middle childhood; (2 examine age-related changes in the neural sensitivity for biological motion, and (3 determine whether neural sensitivity for biological motion relates to social network characteristics in children. Consistent with past work, we demonstrate a significant relation between social network size and neural sensitivity for biological motion in left pSTS, but do not find age-related change in biological motion perception. This finding offers evidence for the interplay between real-world social experiences and functional brain development and has important implications for understanding disorders of atypical social experience. Keywords: Biological motion, Social networks, Middle childhood, Neural specialization, Brain-behavior relations, pSTS

  16. MicroRNA functional network in pancreatic cancer: From biology to ...

    Indian Academy of Sciences (India)

    [Wang J and Sen S 2011 MicroRNA functional network in pancreatic cancer: From biology to biomarkers of disease. ... growth factor type I receptor; INSR, insulin receptor; IPA, Ingenuity Pathway Analysis; IPMN, ..... Prostate cancer signalling.

  17. Exploitation of complex network topology for link prediction in biological interactomes

    KAUST Repository

    Alanis Lobato, Gregorio

    2014-01-01

    In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable

  18. Dosimetry of fast neutrons

    International Nuclear Information System (INIS)

    Jahr, R.

    1975-03-01

    Following an explanation of the physical fundamentals of neutron dosimetry, the special needs in medicine and biology are gone into. It is shown that the dose equivalent used in radiation protection simplifies in an undue manner the complicated dependence of the biological effects. The reason for this is the fact that the RBE for heavy recoil nuclei, amongst others, depends on the energy and sort of particle, whereas it is approximately equal to one for electrons independent of the energy. It is thus necessary in the fields of biology and medicine to have additional information on energy spectra of the neutrons as well as of all charged secondary particles as a function of the position in the phantom. These are obtained partly by calculation and partly by special dosemeters. The accuracy achieved so far is 5%. (ORU/LH) [de

  19. Commentary: Biochemistry and Molecular Biology Educators Launch National Network

    Science.gov (United States)

    Bailey, Cheryl; Bell, Ellis; Johnson, Margaret; Mattos, Carla; Sears, Duane; White, Harold B.

    2010-01-01

    The American Society of Biochemistry and Molecular Biology (ASBMB) has launched an National Science Foundation (NSF)-funded 5 year project to support biochemistry and molecular biology educators learning what and how students learn. As a part of this initiative, hundreds of life scientists will plan and develop a rich central resource for…

  20. A reverse engineering approach to optimize experiments for the construction of biological regulatory networks.

    Science.gov (United States)

    Zhang, Xiaomeng; Shao, Bin; Wu, Yangle; Qi, Ouyang

    2013-01-01

    One of the major objectives in systems biology is to understand the relation between the topological structures and the dynamics of biological regulatory networks. In this context, various mathematical tools have been developed to deduct structures of regulatory networks from microarray expression data. In general, from a single data set, one cannot deduct the whole network structure; additional expression data are usually needed. Thus how to design a microarray expression experiment in order to get the most information is a practical problem in systems biology. Here we propose three methods, namely, maximum distance method, trajectory entropy method, and sampling method, to derive the optimal initial conditions for experiments. The performance of these methods is tested and evaluated in three well-known regulatory networks (budding yeast cell cycle, fission yeast cell cycle, and E. coli. SOS network). Based on the evaluation, we propose an efficient strategy for the design of microarray expression experiments.

  1. On the origin of distribution patterns of motifs in biological networks

    Directory of Open Access Journals (Sweden)

    Lesk Arthur M

    2008-08-01

    Full Text Available Abstract Background Inventories of small subgraphs in biological networks have identified commonly-recurring patterns, called motifs. The inference that these motifs have been selected for function rests on the idea that their occurrences are significantly more frequent than random. Results Our analysis of several large biological networks suggests, in contrast, that the frequencies of appearance of common subgraphs are similar in natural and corresponding random networks. Conclusion Indeed, certain topological features of biological networks give rise naturally to the common appearance of the motifs. We therefore question whether frequencies of occurrences are reasonable evidence that the structures of motifs have been selected for their functional contribution to the operation of networks.

  2. Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

    OpenAIRE

    Shuo Gu; Jianfeng Pei

    2017-01-01

    With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regula...

  3. Neutron Dosimetry

    International Nuclear Information System (INIS)

    Vanhavere, F.

    2001-01-01

    The objective of SCK-CEN's R and D programme on neutron dosimetry is to improve the determination of neutron doses by studying neutron spectra, neutron dosemeters and shielding adaptations. In 2000, R and D focused on the contiued investigation of the bubble detectors type BD-PND and BDT, in particular their sensitivity and temperature dependence; the updating of SCK-CEN's criticality dosemeter, the investigation of the characteristics of new thermoluminescent materials and their use in neutron dosemetry; and the investigation of neutron shielding

  4. Neutron Dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Vanhavere, F

    2001-04-01

    The objective of SCK-CEN's R and D programme on neutron dosimetry is to improve the determination of neutron doses by studying neutron spectra, neutron dosemeters and shielding adaptations. In 2000, R and D focused on the contiued investigation of the bubble detectors type BD-PND and BDT, in particular their sensitivity and temperature dependence; the updating of SCK-CEN's criticality dosemeter, the investigation of the characteristics of new thermoluminescent materials and their use in neutron dosemetry; and the investigation of neutron shielding.

  5. External audit in radiotherapy dosimetry

    International Nuclear Information System (INIS)

    Thwaites, D.I.; Western General Hospital, Edinburgh

    1996-01-01

    Quality audit forms an essential part of any comprehensive quality assurance programme. This is true in radiotherapy generally and in specific areas such as radiotherapy dosimetry. Quality audit can independently test the effectiveness of the quality system and in so doing can identify problem areas and minimize their possible consequences. Some general points concerning quality audit applied to radiotherapy are followed by specific discussion of its practical role in radiotherapy dosimetry, following its evolution from dosimetric intercomparison exercises to routine measurement-based on-going audit in the various developing audit networks both in the UK and internationally. Specific examples of methods and results are given from some of these, including the Scottish+ audit group. Quality audit in radiotherapy dosimetry is now well proven and participation by individual centres is strongly recommended. Similar audit approaches are to be encouraged in other areas of the radiotherapy process. (author)

  6. Fundamentals of Dosimetry. Chapter 3

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimura, E. M. [Universidade de São Paulo, São Paulo (Brazil)

    2014-09-15

    Determination of the energy imparted to matter by radiation is the subject of dosimetry. The energy deposited as radiation interacts with atoms of the material, as seen in the previous chapter. The imparted energy is responsible for the effects that radiation causes in matter, for instance, a rise in temperature, or chemical or physical changes in the material properties. Several of the changes produced in matter by radiation are proportional to the absorbed dose, giving rise to the possibility of using the material as the sensitive part of a dosimeter. Also, the biological effects of radiation depend on the absorbed dose. A set of quantities related to the radiation field is also defined within the scope of dosimetry. It will be shown in this chapter that, under special conditions, there are simple relations between dosimetric and field description quantities. Thus, the framework of dosimetry is the set of physical and operational quantities that are studied in this chapter.

  7. Nonlinear signaling on biological networks: The role of stochasticity and spectral clustering

    Science.gov (United States)

    Hernandez-Hernandez, Gonzalo; Myers, Jesse; Alvarez-Lacalle, Enrique; Shiferaw, Yohannes

    2017-03-01

    Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. It is this nonlinearity that endows biological signaling networks with robust switchlike properties which are critical to their biological function. In this study we investigate how the properties of these signaling systems depend on the network architecture. Our main result is that these nonlinear networks exhibit bistability where the network activity can switch between states that correspond to a low and high activity level. We show that this bistable regime emerges at a critical coupling strength that is determined by the spectral structure of the network. In particular, the set of nodes that correspond to large components of the leading eigenvector of the adjacency matrix determines the onset of bistability. Above this transition the eigenvectors of the adjacency matrix determine a hierarchy of clusters, defined by its spectral properties, which are activated sequentially with increasing network activity. We argue further that the onset of bistability occurs either continuously or discontinuously depending upon whether the leading eigenvector is localized or delocalized. Finally, we show that at low network coupling stochastic transitions to the active branch are also driven by the set of nodes that contribute more strongly to the leading eigenvector. However, at high coupling, transitions are insensitive to network structure since the network can be activated by stochastic transitions of a few nodes. Thus this work identifies important features of biological signaling networks that may underlie their biological

  8. Topics in radiation dosimetry radiation dosimetry

    CERN Document Server

    1972-01-01

    Radiation Dosimetry, Supplement 1: Topics in Radiation Dosimetry covers instruments and techniques in dealing with special dosimetry problems. The book discusses thermoluminescence dosimetry in archeological dating; dosimetric applications of track etching; vacuum chambers of radiation measurement. The text also describes wall-less detectors in microdosimetry; dosimetry of low-energy X-rays; and the theory and general applicability of the gamma-ray theory of track effects to various systems. Dose equivalent determinations in neutron fields by means of moderator techniques; as well as developm

  9. Estimation of dose ionizing radiation exposure by biological dosimetry; Estimación de dosis de exposición a radiaciones ionizantes mediante dosimetría biológica

    Energy Technology Data Exchange (ETDEWEB)

    Herranz Crespo, R.; Moreno Domene, M.; Prieto Rodríguez, M.J.; Lozano Barriuso, M.A.

    2014-07-01

    the Biological Dosimetry Laboratory of the Radiopathology Centre, at Hospital General Universitario Gregorio Marañón, is the only national laboratory accredited by UNE-EN ISO/IEC 17025:2005, and scope to ISO 19238:2004 (Radiation protection – Performance criteria for service laboratories performing biological dosimetry by citogenetics), for dose assessment by the dycentrics assay, has great experience with more than 100 real cases analyzed, and several population studies. This paper describes experience and results from more than 20 years of work under the Reference level II Centre for the attention of irradiated and/or contaminated people. [Spanish] El Laboratorio de Dosimetría Biológica, del Centro de Radiopatología del Hospital General Universitario Gregorio Marañón, es el único en España que dispone de acreditación internacional por la norma UNE-EN ISO/IEC 17025:2005 con alcance a la norma ISO 19238:2004 (Radiationprotection – Performance criteria for service laboratories performing biological dosimetry by citogenetics), para la realización de estimaciones dosimétricas mediante la técnica de dicéntricos, dispone de amplia experiencia en su aplicación en los 110 casos reales analizados, y en diferentes estudios de poblaciones españolas. En este trabajo se describe la experiencia del laboratorio y los resultados obtenidos en los más de 20 años de funcionamiento en el Centro de Referencia de nivel II para la atención a irradiados y/o contaminados por radiaciones ionizantes.

  10. Neural network models: from biology to many - body phenomenology

    International Nuclear Information System (INIS)

    Clark, J.W.

    1993-01-01

    The current surge of research on practical side of neural networks and their utility in memory storage/recall, pattern recognition and classification is given in this article. The initial attraction of neural networks as dynamical and statistical system has been investigated. From the view of many-body theorist, the neurons may be thought of as particles, and the weighted connection between the units, as the interaction between these particles. Finally, the author has seen the impressive capabilities of artificial neural networks in pattern recognition and classification may be exploited to solve data management problems in experimental physics and the discovery of radically new theoretically description of physical problems and neural networks can be used in physics. (A.B.)

  11. Mathematical Analysis of a PDE System for Biological Network Formation

    KAUST Repository

    Haskovec, Jan

    2015-02-04

    Motivated by recent physics papers describing rules for natural network formation, we study an elliptic-parabolic system of partial differential equations proposed by Hu and Cai [13, 15]. The model describes the pressure field thanks to Darcy\\'s type equation and the dynamics of the conductance network under pressure force effects with a diffusion rate D >= 0 representing randomness in the material structure. We prove the existence of global weak solutions and of local mild solutions and study their long term behavior. It turns out that, by energy dissipation, steady states play a central role to understand the network formation capacity of the system. We show that for a large diffusion coefficient D, the zero steady state is stable, while network formation occurs for small values of D due to the instability of the zero steady state, and the borderline case D = 0 exhibits a large class of dynamically stable (in the linearized sense) steady states.

  12. Notes on a PDE system for biological network formation

    KAUST Repository

    Haskovec, Jan; Markowich, Peter A.; Perthame, Benoî t; Schlottbom, Matthias

    2016-01-01

    Darcy’s type equation and the dynamics of the conductance network under pressure force effects. Randomness in the material structure is represented by a linear diffusion term and conductance relaxation by an algebraic decay term. The analytical part

  13. Mathematical Analysis of a PDE System for Biological Network Formation

    KAUST Repository

    Haskovec, Jan; Markowich, Peter A.; Perthame, Benoit

    2015-01-01

    Motivated by recent physics papers describing rules for natural network formation, we study an elliptic-parabolic system of partial differential equations proposed by Hu and Cai [13, 15]. The model describes the pressure field thanks to Darcy's type

  14. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  15. The work programme of EURADOS on internal and external dosimetry.

    Science.gov (United States)

    Rühm, W; Bottollier-Depois, J F; Gilvin, P; Harrison, R; Knežević, Ž; Lopez, M A; Tanner, R; Vargas, A; Woda, C

    2018-01-01

    Since the early 1980s, the European Radiation Dosimetry Group (EURADOS) has been maintaining a network of institutions interested in the dosimetry of ionising radiation. As of 2017, this network includes more than 70 institutions (research centres, dosimetry services, university institutes, etc.), and the EURADOS database lists more than 500 scientists who contribute to the EURADOS mission, which is to promote research and technical development in dosimetry and its implementation into practice, and to contribute to harmonisation of dosimetry in Europe and its conformance with international practices. The EURADOS working programme is organised into eight working groups dealing with environmental, computational, internal, and retrospective dosimetry; dosimetry in medical imaging; dosimetry in radiotherapy; dosimetry in high-energy radiation fields; and harmonisation of individual monitoring. Results are published as freely available EURADOS reports and in the peer-reviewed scientific literature. Moreover, EURADOS organises winter schools and training courses on various aspects relevant for radiation dosimetry, and formulates the strategic research needs in dosimetry important for Europe. This paper gives an overview on the most important EURADOS activities. More details can be found at www.eurados.org .

  16. PyPathway: Python Package for Biological Network Analysis and Visualization.

    Science.gov (United States)

    Xu, Yang; Luo, Xiao-Chun

    2018-05-01

    Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

  17. Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

    Science.gov (United States)

    Beal, Jacob; Lu, Ting; Weiss, Ron

    2011-01-01

    The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks. Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.

  18. BinAligner: a heuristic method to align biological networks.

    Science.gov (United States)

    Yang, Jialiang; Li, Jun; Grünewald, Stefan; Wan, Xiu-Feng

    2013-01-01

    The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species will help detect orthologs and conserved functional modules and provide insights on the evolutionary relationships of the compared species. However, such analyses are not trivial due to the complexity of network and high computational cost. Here we develop a mixture of global and local algorithm, BinAligner, for network alignments. Based on the hypotheses that the similarity between two vertices across networks would be context dependent and that the information from the edges and the structures of subnetworks can be more informative than vertices alone, two scoring schema, 1-neighborhood subnetwork and graphlet, were introduced to derive the scoring matrices between networks, besides the commonly used scoring scheme from vertices. Then the alignment problem is formulated as an assignment problem, which is solved by the combinatorial optimization algorithm, such as the Hungarian method. The proposed algorithm was applied and validated in aligning the protein-protein interaction network of Kaposi's sarcoma associated herpesvirus (KSHV) and that of varicella zoster virus (VZV). Interestingly, we identified several putative functional orthologous proteins with similar functions but very low sequence similarity between the two viruses. For example, KSHV open reading frame 56 (ORF56) and VZV ORF55 are helicase-primase subunits with sequence identity 14.6%, and KSHV ORF75 and VZV ORF44 are tegument proteins with sequence identity 15.3%. These functional pairs can not be identified if one restricts the alignment into orthologous protein pairs. In addition, BinAligner identified a conserved pathway between two viruses, which consists of 7 orthologous protein pairs and these proteins are connected by conserved links. This pathway might be crucial for virus packing and

  19. Modeling Wireless Sensor Networks for Monitoring in Biological Processes

    DEFF Research Database (Denmark)

    Nadimi, Esmaeil

    parameters, as the use of wired sensors is impractical. In this thesis, a ZigBee based wireless sensor network was employed and only a part of the herd was monitored, as monitoring each individual animal in a large herd under practical conditions is inefficient. Investigations to show that the monitored...... (MMAE) approach to the data resulted in the highest classification success rate, due to the use of precise forth-order mathematical models which relate the feed offer to the pitch angle of the neck. This thesis shows that wireless sensor networks can be successfully employed to monitor the behavior...

  20. Robustness leads close to the edge of chaos in coupled map networks: toward the understanding of biological networks

    International Nuclear Information System (INIS)

    Saito, Nen; Kikuchi, Macoto

    2013-01-01

    Dynamics in biological networks are, in general, robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and design systems that are robust against phenotypic perturbations (perturbations in dynamics), as well as systems that are robust against mutation (perturbations in network structure). To achieve such a design, we apply a multicanonical Monte Carlo method. Analysis based on the maximum Lyapunov exponent and parameter sensitivity shows that systems with marginal stability, which are regarded as systems at the edge of chaos, emerge when robustness against network perturbations is required. This emergence of the edge of chaos is a self-organization phenomenon and does not need a fine tuning of parameters. (paper)

  1. Biologically Inspired Target Recognition in Radar Sensor Networks

    Directory of Open Access Journals (Sweden)

    Liang Qilian

    2010-01-01

    Full Text Available One of the great mysteries of the brain is cognitive control. How can the interactions between millions of neurons result in behavior that is coordinated and appears willful and voluntary? There is consensus that it depends on the prefrontal cortex (PFC. Many PFC areas receive converging inputs from at least two sensory modalities. Inspired by human's innate ability to process and integrate information from disparate, network-based sources, we apply human-inspired information integration mechanisms to target detection in cognitive radar sensor network. Humans' information integration mechanisms have been modelled using maximum-likelihood estimation (MLE or soft-max approaches. In this paper, we apply these two algorithms to cognitive radar sensor networks target detection. Discrete-cosine-transform (DCT is used to process the integrated data from MLE or soft-max. We apply fuzzy logic system (FLS to automatic target detection based on the AC power values from DCT. Simulation results show that our MLE-DCT-FLS and soft-max-DCT-FLS approaches perform very well in the radar sensor network target detection, whereas the existing 2D construction algorithm does not work in this study.

  2. Bernstein approximations in glasso-based estimation of biological networks

    NARCIS (Netherlands)

    Purutcuoglu, Vilda; Agraz, Melih; Wit, Ernst

    The Gaussian graphical model (GGM) is one of the common dynamic modelling approaches in the construction of gene networks. In inference of this modelling the interaction between genes can be detected mainly via graphical lasso (glasso) or coordinate descent-based approaches. Although these methods

  3. Cytometric approaches to biological dosimetry

    International Nuclear Information System (INIS)

    Burger, G.

    1983-01-01

    Automatic cytometric techniques for detecting chromosomal aberrations are being tested but will not be used in routine examinations for some time to come. Automatic micronuclei counts are more promising but not sufficiently sensitive in the low dose range ( [de

  4. Radiation dosimetry

    International Nuclear Information System (INIS)

    Harper, M.W.; Thomas, B.; Conway, J.

    1977-01-01

    A dosemeter is described that is based on the TSCD principle (thermally stimulated current dosimetry). Basically this involves irradiating a responsive material and then heating it,whereby an electric current is produced. If the material is heated in an electric field the peak value of the thermally stimulated current or alternatively the total charge released by heating, can be related to the radiation dose received. The instrument described utilises a sheet coated with a thermoplastic polymer, such as a poly4-methylpent-l-ene. The polymer should have a softening point not lower than 150 0 C with an electrical resistivity of at least 10 16 chms/cm at 150 0 C. The polymer may also be PTFE. Heating should be in the range 150 0 C to 200 0 C and the electric field in the range 50 to 10,000V/mm. (U.K.)

  5. Organ dosimetry

    International Nuclear Information System (INIS)

    Kaul, Dean C.; Egbert, Stephen D.; Otis, Mark D.; Kuhn, Thomas; Kerr, George D.; Eckerman, Keith F.; Cristy, Mark; Ryman, Jeffrey C.; Tang, Jabo S.; Maruyama, Takashi

    1987-01-01

    This chapter describes the technical approach, complicating factors, and sensitivities and uncertainties of calculations of doses to the organs of the A-bomb survivors. It is the object of the effort so described to provide data that enables the dosimetry system to determine the fluence, kerma, absorbed dose, and similar quantities in 14 organs and the fetus, specified as being of radiobiological interest. This object was accomplished through the use of adjoint Monte Carlo computations, which use a number of random particle histories to determine the relationship of incident neutrons and gamma rays to those transported to a target organ. The system uses these histories to correlate externally-incident energy- and angle-differential fluences with the fluence spectrum (energy differential only) within the target organ. In order for the system to work in the most efficient manner possible, two levels of data were provided. The first level, represented by approximately 6,000 random adjoint-particle histories, enables the computation of the fluence spectrum with sufficient precision to provide statistically reliable (± 6 %) mean doses within any given organ. With this limited history inventory, the system can be run rapidly for all survivors. Mean organ dose and dose uncertainty are obtainable in this mode. The second mode of operation enables the system to produce a good approximation to fluence spectrum within any organ or to produce the dose in each of an array of organ subvolumes. To be statistically reliable, this level of detail requires far more random histories, approximately 40,000 per organ. Thus, operation of the dosimetry system in this mode (i.e., with this data set) is intended to be on an as-needed, organ-specific basis, since the system run time is eight times that in the mean dose mode. (author)

  6. Building gene co-expression networks using transcriptomics data for systems biology investigations

    DEFF Research Database (Denmark)

    Kadarmideen, Haja; Watson-Haigh, Nathan S.

    2012-01-01

    Gene co-expression networks (GCN), built using high-throughput gene expression data are fundamental aspects of systems biology. The main aims of this study were to compare two popular approaches to building and analysing GCN. We use real ovine microarray transcriptomics datasets representing four......) is connected within a network. The two GCN construction methods used were, Weighted Gene Co-expression Network Analysis (WGCNA) and Partial Correlation and Information Theory (PCIT) methods. Nodes were ranked based on their connectivity measures in each of the four different networks created by WGCNA and PCIT...... (with > 20000 genes) access to large computer clusters, particularly those with larger amounts of shared memory is recommended....

  7. 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

  8. A Reconfigurable and Biologically Inspired Paradigm for Computation Using Network-On-Chip and Spiking Neural Networks

    Directory of Open Access Journals (Sweden)

    Jim Harkin

    2009-01-01

    Full Text Available FPGA devices have emerged as a popular platform for the rapid prototyping of biological Spiking Neural Networks (SNNs applications, offering the key requirement of reconfigurability. However, FPGAs do not efficiently realise the biologically plausible neuron and synaptic models of SNNs, and current FPGA routing structures cannot accommodate the high levels of interneuron connectivity inherent in complex SNNs. This paper highlights and discusses the current challenges of implementing scalable SNNs on reconfigurable FPGAs. The paper proposes a novel field programmable neural network architecture (EMBRACE, incorporating low-power analogue spiking neurons, interconnected using a Network-on-Chip architecture. Results on the evaluation of the EMBRACE architecture using the XOR benchmark problem are presented, and the performance of the architecture is discussed. The paper also discusses the adaptability of the EMBRACE architecture in supporting fault tolerant computing.

  9. Things fall apart: biological species form unconnected parsimony networks.

    Science.gov (United States)

    Hart, Michael W; Sunday, Jennifer

    2007-10-22

    The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.

  10. Probabilistic Inference of Biological Networks via Data Integration

    Directory of Open Access Journals (Sweden)

    Mark F. Rogers

    2015-01-01

    Full Text Available There is significant interest in inferring the structure of subcellular networks of interaction. Here we consider supervised interactive network inference in which a reference set of known network links and nonlinks is used to train a classifier for predicting new links. Many types of data are relevant to inferring functional links between genes, motivating the use of data integration. We use pairwise kernels to predict novel links, along with multiple kernel learning to integrate distinct sources of data into a decision function. We evaluate various pairwise kernels to establish which are most informative and compare individual kernel accuracies with accuracies for weighted combinations. By associating a probability measure with classifier predictions, we enable cautious classification, which can increase accuracy by restricting predictions to high-confidence instances, and data cleaning that can mitigate the influence of mislabeled training instances. Although one pairwise kernel (the tensor product pairwise kernel appears to work best, different kernels may contribute complimentary information about interactions: experiments in S. cerevisiae (yeast reveal that a weighted combination of pairwise kernels applied to different types of data yields the highest predictive accuracy. Combined with cautious classification and data cleaning, we can achieve predictive accuracies of up to 99.6%.

  11. System Biology Approach: Gene Network Analysis for Muscular Dystrophy.

    Science.gov (United States)

    Censi, Federica; Calcagnini, Giovanni; Mattei, Eugenio; Giuliani, Alessandro

    2018-01-01

    Phenotypic changes at different organization levels from cell to entire organism are associated to changes in the pattern of gene expression. These changes involve the entire genome expression pattern and heavily rely upon correlation patterns among genes. The classical approach used to analyze gene expression data builds upon the application of supervised statistical techniques to detect genes differentially expressed among two or more phenotypes (e.g., normal vs. disease). The use of an a posteriori, unsupervised approach based on principal component analysis (PCA) and the subsequent construction of gene correlation networks can shed a light on unexpected behaviour of gene regulation system while maintaining a more naturalistic view on the studied system.In this chapter we applied an unsupervised method to discriminate DMD patient and controls. The genes having the highest absolute scores in the discrimination between the groups were then analyzed in terms of gene expression networks, on the basis of their mutual correlation in the two groups. The correlation network structures suggest two different modes of gene regulation in the two groups, reminiscent of important aspects of DMD pathogenesis.

  12. Novel approaches to develop community-built biological network models for potential drug discovery.

    Science.gov (United States)

    Talikka, Marja; Bukharov, Natalia; Hayes, William S; Hofmann-Apitius, Martin; Alexopoulos, Leonidas; Peitsch, Manuel C; Hoeng, Julia

    2017-08-01

    Hundreds of thousands of data points are now routinely generated in clinical trials by molecular profiling and NGS technologies. A true translation of this data into knowledge is not possible without analysis and interpretation in a well-defined biology context. Currently, there are many public and commercial pathway tools and network models that can facilitate such analysis. At the same time, insights and knowledge that can be gained is highly dependent on the underlying biological content of these resources. Crowdsourcing can be employed to guarantee the accuracy and transparency of the biological content underlining the tools used to interpret rich molecular data. Areas covered: In this review, the authors describe crowdsourcing in drug discovery. The focal point is the efforts that have successfully used the crowdsourcing approach to verify and augment pathway tools and biological network models. Technologies that enable the building of biological networks with the community are also described. Expert opinion: A crowd of experts can be leveraged for the entire development process of biological network models, from ontologies to the evaluation of their mechanistic completeness. The ultimate goal is to facilitate biomarker discovery and personalized medicine by mechanistically explaining patients' differences with respect to disease prevention, diagnosis, and therapy outcome.

  13. Spatial-Frequency Azimuthally Stable Cartography of Biological Polycrystalline Networks

    Directory of Open Access Journals (Sweden)

    V. A. Ushenko

    2013-01-01

    Full Text Available A new azimuthally stable polarimetric technique processing microscopic images of optically anisotropic structures of biological tissues histological sections is proposed. It has been used as a generalized model of phase anisotropy definition of biological tissues by using superposition of Mueller matrices of linear birefringence and optical activity. The matrix element M44 has been chosen as the main information parameter, whose value is independent of the rotation angle of both sample and probing beam polarization plane. For the first time, the technique of concerted spatial-frequency filtration has been used in order to separate the manifestation of linear birefringence and optical activity. Thereupon, the method of azimuthally stable spatial-frequency cartography of biological tissues histological sections has been elaborated. As the analyzing tool, complex statistic, correlation, and fractal analysis of coordinate distributions of M44 element has been performed. The possibility of using the biopsy of the uterine wall tissue in order to differentiate benign (fibromyoma and malignant (adenocarcinoma conditions has been estimated.

  14. A swarm intelligence framework for reconstructing gene networks: searching for biologically plausible architectures.

    Science.gov (United States)

    Kentzoglanakis, Kyriakos; Poole, Matthew

    2012-01-01

    In this paper, we investigate the problem of reverse engineering the topology of gene regulatory networks from temporal gene expression data. We adopt a computational intelligence approach comprising swarm intelligence techniques, namely particle swarm optimization (PSO) and ant colony optimization (ACO). In addition, the recurrent neural network (RNN) formalism is employed for modeling the dynamical behavior of gene regulatory systems. More specifically, ACO is used for searching the discrete space of network architectures and PSO for searching the corresponding continuous space of RNN model parameters. We propose a novel solution construction process in the context of ACO for generating biologically plausible candidate architectures. The objective is to concentrate the search effort into areas of the structure space that contain architectures which are feasible in terms of their topological resemblance to real-world networks. The proposed framework is initially applied to the reconstruction of a small artificial network that has previously been studied in the context of gene network reverse engineering. Subsequently, we consider an artificial data set with added noise for reconstructing a subnetwork of the genetic interaction network of S. cerevisiae (yeast). Finally, the framework is applied to a real-world data set for reverse engineering the SOS response system of the bacterium Escherichia coli. Results demonstrate the relative advantage of utilizing problem-specific knowledge regarding biologically plausible structural properties of gene networks over conducting a problem-agnostic search in the vast space of network architectures.

  15. An attempt to understand glioma stem cell biology through centrality analysis of a protein interaction network.

    Science.gov (United States)

    Mallik, Mrinmay Kumar

    2018-02-07

    Biological networks can be analyzed using "Centrality Analysis" to identify the more influential nodes and interactions in the network. This study was undertaken to create and visualize a biological network comprising of protein-protein interactions (PPIs) amongst proteins which are preferentially over-expressed in glioma cancer stem cell component (GCSC) of glioblastomas as compared to the glioma non-stem cancer cell (GNSC) component and then to analyze this network through centrality analyses (CA) in order to identify the essential proteins in this network and their interactions. In addition, this study proposes a new centrality analysis method pertaining exclusively to transcription factors (TFs) and interactions amongst them. Moreover the relevant molecular functions, biological processes and biochemical pathways amongst these proteins were sought through enrichment analysis. A protein interaction network was created using a list of proteins which have been shown to be preferentially expressed or over-expressed in GCSCs isolated from glioblastomas as compared to the GNSCs. This list comprising of 38 proteins, created using manual literature mining, was submitted to the Reactome FIViz tool, a web based application integrated into Cytoscape, an open source software platform for visualizing and analyzing molecular interaction networks and biological pathways to produce the network. This network was subjected to centrality analyses utilizing ranked lists of six centrality measures using the FIViz application and (for the first time) a dedicated centrality analysis plug-in ; CytoNCA. The interactions exclusively amongst the transcription factors were nalyzed through a newly proposed centrality analysis method called "Gene Expression Associated Degree Centrality Analysis (GEADCA)". Enrichment analysis was performed using the "network function analysis" tool on Reactome. The CA was able to identify a small set of proteins with consistently high centrality ranks that

  16. Neutron spectrometry and dosimetry by means of Bonner spheres system and artificial neural networks applying robust design of artificial neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Martinez B, M.R.; Ortiz R, J.M.; Vega C, H.R. [UAZ, Av. Ramon Lopez Velarde No. 801, 98000 Zacatecas (Mexico)

    2006-07-01

    An Artificial Neural Network has been designed, trained and tested to unfold neutron spectra and simultaneously to calculate equivalent doses. A set of 187 neutron spectra compiled by the International Atomic Energy Agency and 13 equivalent doses were used in the artificial neural network designed, trained and tested. In order to design the neural network was used the robust design of artificial neural networks methodology, which assures that the quality of the neural networks takes into account from the design stage. Unless previous works, here, for first time a group of neural networks were designed and trained to unfold 187 neutron spectra and at the same time to calculate 13 equivalent doses, starting from the count rates coming from the Bonner spheres system by using a systematic and experimental strategy. (Author)

  17. Neutron spectrometry and dosimetry by means of Bonner spheres system and artificial neural networks applying robust design of artificial neural networks

    International Nuclear Information System (INIS)

    Martinez B, M.R.; Ortiz R, J.M.; Vega C, H.R.

    2006-01-01

    An Artificial Neural Network has been designed, trained and tested to unfold neutron spectra and simultaneously to calculate equivalent doses. A set of 187 neutron spectra compiled by the International Atomic Energy Agency and 13 equivalent doses were used in the artificial neural network designed, trained and tested. In order to design the neural network was used the robust design of artificial neural networks methodology, which assures that the quality of the neural networks takes into account from the design stage. Unless previous works, here, for first time a group of neural networks were designed and trained to unfold 187 neutron spectra and at the same time to calculate 13 equivalent doses, starting from the count rates coming from the Bonner spheres system by using a systematic and experimental strategy. (Author)

  18. Quantitative assessment of biological impact using transcriptomic data and mechanistic network models

    International Nuclear Information System (INIS)

    Thomson, Ty M.; Sewer, Alain; Martin, Florian; Belcastro, Vincenzo; Frushour, Brian P.; Gebel, Stephan; Park, Jennifer; Schlage, Walter K.; Talikka, Marja; Vasilyev, Dmitry M.; Westra, Jurjen W.; Hoeng, Julia; Peitsch, Manuel C.

    2013-01-01

    Exposure to biologically active substances such as therapeutic drugs or environmental toxicants can impact biological systems at various levels, affecting individual molecules, signaling pathways, and overall cellular processes. The ability to derive mechanistic insights from the resulting system responses requires the integration of experimental measures with a priori knowledge about the system and the interacting molecules therein. We developed a novel systems biology-based methodology that leverages mechanistic network models and transcriptomic data to quantitatively assess the biological impact of exposures to active substances. Hierarchically organized network models were first constructed to provide a coherent framework for investigating the impact of exposures at the molecular, pathway and process levels. We then validated our methodology using novel and previously published experiments. For both in vitro systems with simple exposure and in vivo systems with complex exposures, our methodology was able to recapitulate known biological responses matching expected or measured phenotypes. In addition, the quantitative results were in agreement with experimental endpoint data for many of the mechanistic effects that were assessed, providing further objective confirmation of the approach. We conclude that our methodology evaluates the biological impact of exposures in an objective, systematic, and quantifiable manner, enabling the computation of a systems-wide and pan-mechanistic biological impact measure for a given active substance or mixture. Our results suggest that various fields of human disease research, from drug development to consumer product testing and environmental impact analysis, could benefit from using this methodology. - Highlights: • The impact of biologically active substances is quantified at multiple levels. • The systems-level impact integrates the perturbations of individual networks. • The networks capture the relationships between

  19. Robust Learning of High-dimensional Biological Networks with Bayesian Networks

    Science.gov (United States)

    Nägele, Andreas; Dejori, Mathäus; Stetter, Martin

    Structure learning of Bayesian networks applied to gene expression data has become a potentially useful method to estimate interactions between genes. However, the NP-hardness of Bayesian network structure learning renders the reconstruction of the full genetic network with thousands of genes unfeasible. Consequently, the maximal network size is usually restricted dramatically to a small set of genes (corresponding with variables in the Bayesian network). Although this feature reduction step makes structure learning computationally tractable, on the downside, the learned structure might be adversely affected due to the introduction of missing genes. Additionally, gene expression data are usually very sparse with respect to the number of samples, i.e., the number of genes is much greater than the number of different observations. Given these problems, learning robust network features from microarray data is a challenging task. This chapter presents several approaches tackling the robustness issue in order to obtain a more reliable estimation of learned network features.

  20. Reverse engineering biological networks :applications in immune responses to bio-toxins.

    Energy Technology Data Exchange (ETDEWEB)

    Martino, Anthony A.; Sinclair, Michael B.; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Thomas, Edward Victor; Slepoy, Alexander; Zhang, Zhaoduo; May, Elebeoba Eni; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-12-01

    Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.

  1. Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

    Directory of Open Access Journals (Sweden)

    Lo Kenneth

    2012-08-01

    Full Text Available Abstract Background Inference about regulatory networks from high-throughput genomics data is of great interest in systems biology. We present a Bayesian approach to infer gene regulatory networks from time series expression data by integrating various types of biological knowledge. Results We formulate network construction as a series of variable selection problems and use linear regression to model the data. Our method summarizes additional data sources with an informative prior probability distribution over candidate regression models. We extend the Bayesian model averaging (BMA variable selection method to select regulators in the regression framework. We summarize the external biological knowledge by an informative prior probability distribution over the candidate regression models. Conclusions We demonstrate our method on simulated data and a set of time-series microarray experiments measuring the effect of a drug perturbation on gene expression levels, and show that it outperforms leading regression-based methods in the literature.

  2. Deep Neural Networks: A New Framework for Modeling Biological Vision and Brain Information Processing.

    Science.gov (United States)

    Kriegeskorte, Nikolaus

    2015-11-24

    Recent advances in neural network modeling have enabled major strides in computer vision and other artificial intelligence applications. Human-level visual recognition abilities are coming within reach of artificial systems. Artificial neural networks are inspired by the brain, and their computations could be implemented in biological neurons. Convolutional feedforward networks, which now dominate computer vision, take further inspiration from the architecture of the primate visual hierarchy. However, the current models are designed with engineering goals, not to model brain computations. Nevertheless, initial studies comparing internal representations between these models and primate brains find surprisingly similar representational spaces. With human-level performance no longer out of reach, we are entering an exciting new era, in which we will be able to build biologically faithful feedforward and recurrent computational models of how biological brains perform high-level feats of intelligence, including vision.

  3. Secondary standard dosimetry laboratories: Development and trends

    International Nuclear Information System (INIS)

    1985-08-01

    This publication describes the work of the IAEA and the WHO in the establishment of a network of Secondary Standard Dosimetry Laboratories. Membership in the SSDL network has now risen to about 50 laboratories, of which 36 are in developing countries

  4. Causal inference in biology networks with integrated belief propagation.

    Science.gov (United States)

    Chang, Rui; Karr, Jonathan R; Schadt, Eric E

    2015-01-01

    Inferring causal relationships among molecular and higher order phenotypes is a critical step in elucidating the complexity of living systems. Here we propose a novel method for inferring causality that is no longer constrained by the conditional dependency arguments that limit the ability of statistical causal inference methods to resolve causal relationships within sets of graphical models that are Markov equivalent. Our method utilizes Bayesian belief propagation to infer the responses of perturbation events on molecular traits given a hypothesized graph structure. A distance measure between the inferred response distribution and the observed data is defined to assess the 'fitness' of the hypothesized causal relationships. To test our algorithm, we infer causal relationships within equivalence classes of gene networks in which the form of the functional interactions that are possible are assumed to be nonlinear, given synthetic microarray and RNA sequencing data. We also apply our method to infer causality in real metabolic network with v-structure and feedback loop. We show that our method can recapitulate the causal structure and recover the feedback loop only from steady-state data which conventional method cannot.

  5. Integrated analysis of multiple data sources reveals modular structure of biological networks

    International Nuclear Information System (INIS)

    Lu Hongchao; Shi Baochen; Wu Gaowei; Zhang Yong; Zhu Xiaopeng; Zhang Zhihua; Liu Changning; Zhao, Yi; Wu Tao; Wang Jie; Chen Runsheng

    2006-01-01

    It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

  6. Personnel neutron dosimetry

    International Nuclear Information System (INIS)

    Hankins, D.

    1982-04-01

    This edited transcript of a presentation on personnel neutron discusses the accuracy of present dosimetry practices, requirements, calibration, dosemeter types, quality factors, operational problems, and dosimetry for a criticality accident. 32 figs

  7. An appraisal of biological responses and network of environmental interactions in non-mining and mining impacted coastal waters

    Digital Repository Service at National Institute of Oceanography (India)

    Fernandes, C.E.G.; Malik, A; Jineesh, V.K.; Fernandes, S.O.; Das, A; Pandey, S.S.; Kanolkar, G.; Sujith, P.P.; Velip, D.; Shaikh, S.; Helekar, S.; Gonsalves, M.J.B.D.; Nair, S.; LokaBharathi, P.A

    iron brought from the hinterlands. We hypothesize that there could be a shift in biological response along with changes in network of interactions between environmental and biological variables in these mining and non-mining impacted regions, lying 160...

  8. Exploitation of complex network topology for link prediction in biological interactomes

    KAUST Repository

    Alanis Lobato, Gregorio

    2014-06-01

    The network representation of the interactions between proteins and genes allows for a holistic perspective of the complex machinery underlying the living cell. However, the large number of interacting entities within the cell makes network construction a daunting and arduous task, prone to errors and missing information. Fortunately, the structure of biological networks is not different from that of other complex systems, such as social networks, the world-wide web or power grids, for which growth models have been proposed to better understand their structure and function. This means that we can design tools based on these models in order to exploit the topology of biological interactomes with the aim to construct more complete and reliable maps of the cell. In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable and biologically meaningful information that enriches the datasets to which we have access today.

  9. Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

    Science.gov (United States)

    Chen, Bor-Sen; Yeh, Chin-Hsun

    2017-12-01

    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Dosimetry for radiation processing

    DEFF Research Database (Denmark)

    Miller, Arne

    1986-01-01

    During the past few years significant advances have taken place in the different areas of dosimetry for radiation processing, mainly stimulated by the increased interest in radiation for food preservation, plastic processing and sterilization of medical products. Reference services both...... and sterilization dosimetry, optichromic dosimeters in the shape of small tubes for food processing, and ESR spectroscopy of alanine for reference dosimetry. In this paper the special features of radiation processing dosimetry are discussed, several commonly used dosimeters are reviewed, and factors leading...

  11. Wavelet analysis of polarization maps of polycrystalline biological fluids networks

    Science.gov (United States)

    Ushenko, Y. A.

    2011-12-01

    The optical model of human joints synovial fluid is proposed. The statistic (statistic moments), correlation (autocorrelation function) and self-similar (Log-Log dependencies of power spectrum) structure of polarization two-dimensional distributions (polarization maps) of synovial fluid has been analyzed. It has been shown that differentiation of polarization maps of joint synovial fluid with different physiological state samples is expected of scale-discriminative analysis. To mark out of small-scale domain structure of synovial fluid polarization maps, the wavelet analysis has been used. The set of parameters, which characterize statistic, correlation and self-similar structure of wavelet coefficients' distributions of different scales of polarization domains for diagnostics and differentiation of polycrystalline network transformation connected with the pathological processes, has been determined.

  12. A framework to find the logic backbone of a biological network.

    Science.gov (United States)

    Maheshwari, Parul; Albert, Réka

    2017-12-06

    Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean modeling, can obtain their attractors (which correspond to cell types and behaviors) and their trajectories from an initial state (e.g. a resting state) to the attractors, for example in response to an external signal. The existing methods however do not elucidate the causal relationships between distant nodes in the network. In this work, we propose a simple logic framework, based on categorizing causal relationships as sufficient or necessary, as a complement to Boolean networks. We identify and explore the properties of complex subnetworks that are distillable into a single logic relationship. We also identify cyclic subnetworks that ensure the stabilization of the state of participating nodes regardless of the rest of the network. We identify the logic backbone of biomolecular networks, consisting of external signals, self-sustaining cyclic subnetworks (stable motifs), and output nodes. Furthermore, we use the logic framework to identify crucial nodes whose override can drive the system from one steady state to another. We apply these techniques to two biological networks: the epithelial-to-mesenchymal transition network corresponding to a developmental process exploited in tumor invasion, and the network of abscisic acid induced stomatal closure in plants. We find interesting subnetworks with logical implications in these networks. Using these subgraphs and motifs, we efficiently reduce both networks to succinct backbone structures. The logic representation identifies the causal relationships between distant nodes and subnetworks. This knowledge can form the basis of network control or used in the reverse engineering of networks.

  13. A biologically inspired neural network controller for ballistic arm movements

    Directory of Open Access Journals (Sweden)

    Schmid Maurizio

    2007-09-01

    Full Text Available Abstract Background In humans, the implementation of multijoint tasks of the arm implies a highly complex integration of sensory information, sensorimotor transformations and motor planning. Computational models can be profitably used to better understand the mechanisms sub-serving motor control, thus providing useful perspectives and investigating different control hypotheses. To this purpose, the use of Artificial Neural Networks has been proposed to represent and interpret the movement of upper limb. In this paper, a neural network approach to the modelling of the motor control of a human arm during planar ballistic movements is presented. Methods The developed system is composed of three main computational blocks: 1 a parallel distributed learning scheme that aims at simulating the internal inverse model in the trajectory formation process; 2 a pulse generator, which is responsible for the creation of muscular synergies; and 3 a limb model based on two joints (two degrees of freedom and six muscle-like actuators, that can accommodate for the biomechanical parameters of the arm. The learning paradigm of the neural controller is based on a pure exploration of the working space with no feedback signal. Kinematics provided by the system have been compared with those obtained in literature from experimental data of humans. Results The model reproduces kinematics of arm movements, with bell-shaped wrist velocity profiles and approximately straight trajectories, and gives rise to the generation of synergies for the execution of movements. The model allows achieving amplitude and direction errors of respectively 0.52 cm and 0.2 radians. Curvature values are similar to those encountered in experimental measures with humans. The neural controller also manages environmental modifications such as the insertion of different force fields acting on the end-effector. Conclusion The proposed system has been shown to properly simulate the development of

  14. Contribution of new cytogenetic techniques in the estimations of old irradiations in retrospective biological dosimetry; Apport des nouvelles techniques de cytogenetiques dans l'estimation des irradiations anciennes en dosimetrie biologique retrospective

    Energy Technology Data Exchange (ETDEWEB)

    Pouzoulet, F

    2007-10-15

    The objective of this study was to answer three questions: if the translocations are steady: the results have shown that the translocations even if they are not obligatory steady can be used in retrospective dosimetry. Furthermore, it appeared important to consider the complex translocations in view of their relative stability and complementary information they bring ( quality of radiation, received dose). The second question is what contribution of the M-F.I.S.H. in the translocations analysis in comparison with the F.I.S.H.-3: we have shown that the M-F.I.S.H. would allow to raise the whole of doubt due to a partial genome observation. that has for effect to increase the precision of the analysis and that what ever be the received dose. The third question is if there are differences between the chromosomal aberrations generated by x radiation of 50 keV and by gamma radiation from cobalt-60: yes, the low energy photons generate more translocations than the photons coming from cobalt-60. But they generate less dicentrics. this difference comes from the way the energy is deposited that leads to a more important formation of complex and multiple translocations with the low energy photons. this could constitute a problem in the use of low energy photons in radiotherapy. it would seem that the simple translocations rate is not influenced by the photons energy. (N.C.)

  15. Contribution of new cytogenetic techniques in the estimations of old irradiations in retrospective biological dosimetry; Apport des nouvelles techniques de cytogenetiques dans l'estimation des irradiations anciennes en dosimetrie biologique retrospective

    Energy Technology Data Exchange (ETDEWEB)

    Pouzoulet, F

    2007-10-15

    The objective of this study was to answer three questions: if the translocations are steady: the results have shown that the translocations even if they are not obligatory steady can be used in retrospective dosimetry. Furthermore, it appeared important to consider the complex translocations in view of their relative stability and complementary information they bring ( quality of radiation, received dose). The second question is what contribution of the M-F.I.S.H. in the translocations analysis in comparison with the F.I.S.H.-3: we have shown that the M-F.I.S.H. would allow to raise the whole of doubt due to a partial genome observation. that has for effect to increase the precision of the analysis and that what ever be the received dose. The third question is if there are differences between the chromosomal aberrations generated by x radiation of 50 keV and by gamma radiation from cobalt-60: yes, the low energy photons generate more translocations than the photons coming from cobalt-60. But they generate less dicentrics. this difference comes from the way the energy is deposited that leads to a more important formation of complex and multiple translocations with the low energy photons. this could constitute a problem in the use of low energy photons in radiotherapy. it would seem that the simple translocations rate is not influenced by the photons energy. (N.C.)

  16. RANKING RELATIONS USING ANALOGIES IN BIOLOGICAL AND INFORMATION NETWORKS1

    Science.gov (United States)

    Silva, Ricardo; Heller, Katherine; Ghahramani, Zoubin; Airoldi, Edoardo M.

    2013-01-01

    Analogical reasoning depends fundamentally on the ability to learn and generalize about relations between objects. We develop an approach to relational learning which, given a set of pairs of objects S = {A(1) : B(1), A(2) : B(2), …, A(N) : B(N)}, measures how well other pairs A : B fit in with the set S. Our work addresses the following question: is the relation between objects A and B analogous to those relations found in S? Such questions are particularly relevant in information retrieval, where an investigator might want to search for analogous pairs of objects that match the query set of interest. There are many ways in which objects can be related, making the task of measuring analogies very challenging. Our approach combines a similarity measure on function spaces with Bayesian analysis to produce a ranking. It requires data containing features of the objects of interest and a link matrix specifying which relationships exist; no further attributes of such relationships are necessary. We illustrate the potential of our method on text analysis and information networks. An application on discovering functional interactions between pairs of proteins is discussed in detail, where we show that our approach can work in practice even if a small set of protein pairs is provided. PMID:24587838

  17. Chemical dosimetry principles in high dose dosimetry

    International Nuclear Information System (INIS)

    Mhatre, Sachin G.V.

    2016-01-01

    In radiation processing, activities of principal concern are process validation and process control. The objective of such formalized procedures is to establish documentary evidence that the irradiation process has achieved the desired results. The key element of such activities is inevitably a well characterized reliable dosimetry system that is traceable to recognized national and international dosimetry standards. Only such dosimetry systems can help establish the required documentary evidence. In addition, industrial radiation processing such as irradiation of foodstuffs and sterilization of health careproducts are both highly regulated, in particular with regard to dose. Besides, dosimetry is necessary for scaling up processes from the research level to the industrial level. Thus, accurate dosimetry is indispensable

  18. Structural identifiability of cyclic graphical models of biological networks with latent variables.

    Science.gov (United States)

    Wang, Yulin; Lu, Na; Miao, Hongyu

    2016-06-13

    Graphical models have long been used to describe biological networks for a variety of important tasks such as the determination of key biological parameters, and the structure of graphical model ultimately determines whether such unknown parameters can be unambiguously obtained from experimental observations (i.e., the identifiability problem). Limited by resources or technical capacities, complex biological networks are usually partially observed in experiment, which thus introduces latent variables into the corresponding graphical models. A number of previous studies have tackled the parameter identifiability problem for graphical models such as linear structural equation models (SEMs) with or without latent variables. However, the limited resolution and efficiency of existing approaches necessarily calls for further development of novel structural identifiability analysis algorithms. An efficient structural identifiability analysis algorithm is developed in this study for a broad range of network structures. The proposed method adopts the Wright's path coefficient method to generate identifiability equations in forms of symbolic polynomials, and then converts these symbolic equations to binary matrices (called identifiability matrix). Several matrix operations are introduced for identifiability matrix reduction with system equivalency maintained. Based on the reduced identifiability matrices, the structural identifiability of each parameter is determined. A number of benchmark models are used to verify the validity of the proposed approach. Finally, the network module for influenza A virus replication is employed as a real example to illustrate the application of the proposed approach in practice. The proposed approach can deal with cyclic networks with latent variables. The key advantage is that it intentionally avoids symbolic computation and is thus highly efficient. Also, this method is capable of determining the identifiability of each single parameter and

  19. A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

    Science.gov (United States)

    Kang, Tianyu; Ding, Wei; Zhang, Luoyan; Ziemek, Daniel; Zarringhalam, Kourosh

    2017-12-19

    Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers. In this paper, we develop a biological network-based regularized artificial neural network model for prediction of phenotype from transcriptomic measurements in clinical trials. To improve model sparsity and the overall reproducibility of the model, we incorporate regularization for simultaneous shrinkage of gene sets based on active upstream regulatory mechanisms into the model. We benchmark our method against various regression, support vector machines and artificial neural network models and demonstrate the ability of our method in predicting the clinical outcomes using clinical trial data on acute rejection in kidney transplantation and response to Infliximab in ulcerative colitis. We show that integration of prior biological knowledge into the classification as developed in this paper, significantly improves the robustness and generalizability of predictions to independent datasets. We provide a Java code of our algorithm along with a parsed version of the STRING DB database. In summary, we present a method for prediction of clinical phenotypes using baseline genome-wide expression data that makes use of prior biological knowledge on gene-regulatory interactions in order to increase robustness and reproducibility of omic-scale markers. The integrated group-wise regularization methods increases the interpretability of biological signatures and gives stable performance estimates across independent test sets.

  20. 10 CFR 835.1304 - Nuclear accident dosimetry.

    Science.gov (United States)

    2010-01-01

    ...) Methods and equipment for analysis of biological materials; (3) A system of fixed nuclear accident... Nuclear accident dosimetry. (a) Installations possessing sufficient quantities of fissile material to... 10 Energy 4 2010-01-01 2010-01-01 false Nuclear accident dosimetry. 835.1304 Section 835.1304...

  1. Dosimetry system 1986

    International Nuclear Information System (INIS)

    Woolson, William A.; Egbert, Stephen D.; Gritzner, Michael L.

    1987-01-01

    In May 1983, the authors proposed a dosimetry system for use by the Radiation Effects Research Foundation (RERF) that would incorporate the new findings and calculations of the joint United States - Japan working groups on the reassessment of A-bomb dosimetry. The proposed dosimetry system evolved from extensive discussions with RERF personnel, numerous meetings of the scientists from Japan and the United States involved in the dosimetry reassessment research, and requirements expressed by epidemiologists and radiobiologists on the various review panels. The dosimetry system proposed was based on considerations of the dosimetry requirements for the normal work of RERF and for future research in radiobiology, the computerized input data on A-bomb survivors available in the RERF data base, the level of detail, precision, and accuracy of various components of the dosimetric estimates, and the computer resources available at RERF in Hiroshima. These discussions and our own experience indicated that, in light of the expansion of computer and radiation technologies and the desire for more detail in the dosimetry, an entirely new approach to the dosimetry system was appropriate. This resulted in a complete replacement of the T65D system as distinguished from a simpler approach involving a renormalization of T65D parameters to reflect the new dosimetry. The proposed dosimetry system for RERF and the plan for implementation was accepted by the Department of Energy (DOE) Working Group on A-bomb Dosimetry chaired by Dr. R.F. Christy. The dosimetry system plan was also presented to the binational A-bomb dosimetry review groups for critical comment and was discussed at joint US-Japan workshop. A prototype dosimetry system incorporating preliminary dosimetry estimates and applicable to only a limited set of A-bomb survivors was installed on the RERF computer system in the fall of 1984. This system was successfully operated at RERF and provided an initial look at the impact of

  2. Applications of gel dosimetry

    International Nuclear Information System (INIS)

    Ibbott, Geoffrey S

    2004-01-01

    Gel dosimetry has been examined as a clinical dosimeter since the 1950s. During the last two decades, however, a rapid increase in the number of investigators has been seen, and the body of knowledge regarding gel dosimetry has expanded considerably. Gel dosimetry is still considered a research project, and the introduction of this tool into clinical use is proceeding slowly. This paper will review the characteristics of gel dosimetry that make it desirable for clinical use, the postulated and demonstrated applications of gel dosimetry, and some complications, set-backs, and failures that have contributed to the slow introduction into routine clinical use

  3. Proposal of a New Method for Neutron Dosimetry Based on Spectral Information Obtained by Application of Artificial Neural Networks

    International Nuclear Information System (INIS)

    Fehrenbacher, G.; Schuetz, R.; Hahn, K.; Sprunck, M.; Cordes, E.; Biersack, J.P.; Wahl, W.

    1999-01-01

    A new method for the monitoring of neutron radiation is proposed. It is based on the determination of spectral information on the neutron field in order to derive dose quantities like the ambient dose equivalent, the dose equivalent, or other dose quantities which depend on the neutron energy. The method uses a multi-element system consisting of converter type silicon detectors. The unfolding procedure is based on an artificial neural network (ANN). The response function of each element is determined by a computational model considering the neutron interaction with the dosemeter layers and the subsequent transport of produced ions. An example is given for a multi-element system. The ANN is trained by a given set of neutron spectra and then applied to count responses obtained in neutron fields. Four examples of spectra unfolded using the ANN are presented. (author)

  4. Biological network extraction from scientific literature: state of the art and challenges.

    Science.gov (United States)

    Li, Chen; Liakata, Maria; Rebholz-Schuhmann, Dietrich

    2014-09-01

    Networks of molecular interactions explain complex biological processes, and all known information on molecular events is contained in a number of public repositories including the scientific literature. Metabolic and signalling pathways are often viewed separately, even though both types are composed of interactions involving proteins and other chemical entities. It is necessary to be able to combine data from all available resources to judge the functionality, complexity and completeness of any given network overall, but especially the full integration of relevant information from the scientific literature is still an ongoing and complex task. Currently, the text-mining research community is steadily moving towards processing the full body of the scientific literature by making use of rich linguistic features such as full text parsing, to extract biological interactions. The next step will be to combine these with information from scientific databases to support hypothesis generation for the discovery of new knowledge and the extension of biological networks. The generation of comprehensive networks requires technologies such as entity grounding, coordination resolution and co-reference resolution, which are not fully solved and are required to further improve the quality of results. Here, we analyse the state of the art for the extraction of network information from the scientific literature and the evaluation of extraction methods against reference corpora, discuss challenges involved and identify directions for future research. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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

    Science.gov (United States)

    He, Fei; Murabito, Ettore; Westerhoff, Hans V

    2016-04-01

    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 through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. © 2016 The Author(s).

  6. Personal dosimetry service of VF, a.s. company

    International Nuclear Information System (INIS)

    Prasek, P.

    2009-01-01

    The VF, a.s. Company will extend its services in the area of personal dosimetry at the end of 2008, which is fully in compliance with the requirements of the Atomic Act, section 9 paragraph (1) letter r) and Decree on Radiation Protection, section 59 paragraph (1) letter a). Optically stimulated luminescence was selected in VF .a.s. as the most advantageous and the most advanced technology for the integral personal dosimetry. Optically stimulated luminescence (OSL) has been using in dosimetry for more than ten years. Although it is relatively new technology , its indisputable advantages predetermine that technology has significantly benefited in personal dosimetry services within a short time all over the advanced world. The VF, a.s. personal dosimetry service is based on the licensed products of LANDAUER, the US company, which is the world leader in OSL dosimetry. Crystalline Al 2 O 3 :C was selected as the detection material. All equipment of personal dosimetry service is installed in the VF Centre of Technology in Cerna Hora. The personal dosimetry service is incorporated in the International LANDAUER Dosimetry Service Network, and in the European Union, it is directly linked to the LANDAUER European Headquarters with its office in Paris. As a part of the OSL technology licence, the VF personal dosimetry service was included in the inter-laboratory comparison programme of the LANDAUER syndicate. (author)

  7. Personal dosimetry service of VF, a.s. company

    International Nuclear Information System (INIS)

    Prasek, P.

    2008-01-01

    The VF, a.s. Company will extend its services in the area of personal dosimetry at the end of 2008, which is fully in compliance with the requirements of the Atomic Act, section 9 paragraph (1) letter r) and Decree on Radiation Protection, section 59 paragraph (1) letter a). Optically stimulated luminescence was selected in VF .a.s. as the most advantageous and the most advanced technology for the integral personal dosimetry . Optically stimulated luminescence (OSL) has been using in dosimetry for more than ten years. Although it is relatively new technology , its indisputable advantages predetermine that technology has significantly benefited in personal dosimetry services within a short time all over the advanced world. The VF, a.s. personal dosimetry service is based on the licensed products of LANDAUER, the US company, which is the world leader in OSL dosimetry. Crystalline Al 2 O 3 :C was selected as the detection material. All equipment of personal dosimetry service is installed in the VF Centre of Technology in Cerna Hora. The personal dosimetry service is incorporated in the International LANDAUER Dosimetry Service Network, and in the European Union, it is directly linked to the LANDAUER European Headquarters with its office in Paris. As a part of the OSL technology licence, the VF personal dosimetry service was included in the inter-laboratory comparison programme of the LANDAUER syndicate. (author)

  8. Root Systems Biology: Integrative Modeling across Scales, from Gene Regulatory Networks to the Rhizosphere1

    Science.gov (United States)

    Hill, Kristine; Porco, Silvana; Lobet, Guillaume; Zappala, Susan; Mooney, Sacha; Draye, Xavier; Bennett, Malcolm J.

    2013-01-01

    Genetic and genomic approaches in model organisms have advanced our understanding of root biology over the last decade. Recently, however, systems biology and modeling have emerged as important approaches, as our understanding of root regulatory pathways has become more complex and interpreting pathway outputs has become less intuitive. To relate root genotype to phenotype, we must move beyond the examination of interactions at the genetic network scale and employ multiscale modeling approaches to predict emergent properties at the tissue, organ, organism, and rhizosphere scales. Understanding the underlying biological mechanisms and the complex interplay between systems at these different scales requires an integrative approach. Here, we describe examples of such approaches and discuss the merits of developing models to span multiple scales, from network to population levels, and to address dynamic interactions between plants and their environment. PMID:24143806

  9. VANESA - A Software Application for the Visualization and Analysis of Networks in Systems Biology Applications

    Directory of Open Access Journals (Sweden)

    Brinkrolf Christoph

    2014-06-01

    Full Text Available VANESA is a modeling software for the automatic reconstruction and analysis of biological networks based on life-science database information. Using VANESA, scientists are able to model any kind of biological processes and systems as biological networks. It is now possible for scientists to automatically reconstruct important molecular systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA. Additionally, experimental results can be expanded with database information to better analyze the investigated elements and processes in an overall context. Users also have the possibility to use graph theoretical approaches in VANESA to identify regulatory structures and significant actors within the modeled systems. These structures can then be further investigated in the Petri net environment of VANESA. It is platform-independent, free-of-charge, and available at http://vanesa.sf.net.

  10. Systems Biology Modeling of the Radiation Sensitivity Network: A Biomarker Discovery Platform

    International Nuclear Information System (INIS)

    Eschrich, Steven; Zhang Hongling; Zhao Haiyan; Boulware, David; Lee, Ji-Hyun; Bloom, Gregory; Torres-Roca, Javier F.

    2009-01-01

    Purpose: The discovery of effective biomarkers is a fundamental goal of molecular medicine. Developing a systems-biology understanding of radiosensitivity can enhance our ability of identifying radiation-specific biomarkers. Methods and Materials: Radiosensitivity, as represented by the survival fraction at 2 Gy was modeled in 48 human cancer cell lines. We applied a linear regression algorithm that integrates gene expression with biological variables, including ras status (mut/wt), tissue of origin and p53 status (mut/wt). Results: The biomarker discovery platform is a network representation of the top 500 genes identified by linear regression analysis. This network was reduced to a 10-hub network that includes c-Jun, HDAC1, RELA (p65 subunit of NFKB), PKC-beta, SUMO-1, c-Abl, STAT1, AR, CDK1, and IRF1. Nine targets associated with radiosensitization drugs are linked to the network, demonstrating clinical relevance. Furthermore, the model identified four significant radiosensitivity clusters of terms and genes. Ras was a dominant variable in the analysis, as was the tissue of origin, and their interaction with gene expression but not p53. Overrepresented biological pathways differed between clusters but included DNA repair, cell cycle, apoptosis, and metabolism. The c-Jun network hub was validated using a knockdown approach in 8 human cell lines representing lung, colon, and breast cancers. Conclusion: We have developed a novel radiation-biomarker discovery platform using a systems biology modeling approach. We believe this platform will play a central role in the integration of biology into clinical radiation oncology practice.

  11. Evaluation of gene association methods for coexpression network construction and biological knowledge discovery.

    Directory of Open Access Journals (Sweden)

    Sapna Kumari

    Full Text Available BACKGROUND: Constructing coexpression networks and performing network analysis using large-scale gene expression data sets is an effective way to uncover new biological knowledge; however, the methods used for gene association in constructing these coexpression networks have not been thoroughly evaluated. Since different methods lead to structurally different coexpression networks and provide different information, selecting the optimal gene association method is critical. METHODS AND RESULTS: In this study, we compared eight gene association methods - Spearman rank correlation, Weighted Rank Correlation, Kendall, Hoeffding's D measure, Theil-Sen, Rank Theil-Sen, Distance Covariance, and Pearson - and focused on their true knowledge discovery rates in associating pathway genes and construction coordination networks of regulatory genes. We also examined the behaviors of different methods to microarray data with different properties, and whether the biological processes affect the efficiency of different methods. CONCLUSIONS: We found that the Spearman, Hoeffding and Kendall methods are effective in identifying coexpressed pathway genes, whereas the Theil-sen, Rank Theil-Sen, Spearman, and Weighted Rank methods perform well in identifying coordinated transcription factors that control the same biological processes and traits. Surprisingly, the widely used Pearson method is generally less efficient, and so is the Distance Covariance method that can find gene pairs of multiple relationships. Some analyses we did clearly show Pearson and Distance Covariance methods have distinct behaviors as compared to all other six methods. The efficiencies of different methods vary with the data properties to some degree and are largely contingent upon the biological processes, which necessitates the pre-analysis to identify the best performing method for gene association and coexpression network construction.

  12. Scientific days on electromagnetic fields: from dosimetry to human health - Conference proceedings; Journees scientifiques - Champs electromagnetiques: de la dosimetrie a la sante humaine - Recueil des resumes et presentations

    Energy Technology Data Exchange (ETDEWEB)

    Wiart, J.; Ghanmi, A.; Picon, O.; Conil, E.; Varsier, N.; Hadjem, A.; Sudret, B.; Magne, I.; Souques, M.; Gaudaire, F.; De Seze, R.; Jawad, O.; Lautru, D.; Dricot, J.M.; Horlin, F.; De Doncker, P.; Drissaoui, A.; Musy, F.; Nicolas, L.; Perrussel, R.; Scorretti, R.; Voyer, D.; Jala, M.; Moulines, E.; Levy-Leduc, C.; Mahfouz, Z.; Gati, A.; Fouad Hanna, V.; Leveque, P.; Arnaud-Cormos, D.; Zhadobov, M.; Jarrige, P.; Gaborit, G.; Kohler, S.; Ticaud, N.; Duvillaret, L.; Guelilia, Z.; Loison, R.; Gillard, R.; Laisne, A.; Favet, D.; Benadhira, R.; Mir, L.; Nadi, M.; Kourtiche, D.; Gazeau, F.; Wilhelm, C.; Delemotte, L.; Breton, M.; Tarek, M.; Marc-Vergnes, J.P.; Yardin, C.; Perrin, A.; Le Drean, Y.; Sauleau, R.; Lambrozo, J.; Selmaoui, B.; Ghosn, R.; Thuroczy, G.; Villegier, A.S.; Loos, N.; Brenet-Dufour, V.; Liabeuf, S.; Bach, V.; Moretti, D.; Lewis, N.; Garenne, A.; Poulletier De Gannes, F.; Haro, E.; Lagroye, I.; Bornat, Y.; Boutaib, Y.; Saighi, S.; Renaud, S.; Veyre, B.; Schuz, J.; Deltour, I.; Van Deventer, E.; Vecchia, P.; Merckel, O.; Bellaouel, A.; Demaret, P.; Donati, P.; Jovanovic, D.; Chauvin, S.; Desreumaux, J.P.; Fouquet, L.; Picard, D.; Massardier-Pilonchery, A.; Hours, M.; Bergeret, A.; Person, C.; Toutain, Y.; Butet, R.; Berrahma, K.; Balderelli, I.; Stelmaszyk, V.; Cretallaz, C.; Lamproglou, I.; Amourette, C.; Diserbo, M.; Fauquette, W.; Martigne, P.; Collin, A.; Lagroye, I.; Ait Aissa, S.; Hurtier, A.; Taxile, M.; Le Montagner, L.; Athane, A.; Duleu, S.; Percherancier, Y.; Geffard, M.; Ruffie, G.; Billaudel, B.; Veyret, B.; Pelletier, A.; Delanaud, S.; Libert, J.P.; Schunck, T.; Bieth, F.; Soubere Mahamoud, Y.; Le Quement, C.; Ferrand, G.; Le Guevel, R.; Carton, P.H.; Luong, M.; Tanvir, S.; Selmaoui, B.; Silva Pires-Antonietti, V.; Sonnet, P.; Pulvin, S.; Kuster, O.; Tetelin, C.

    2012-04-15

    This document brings together the available presentations (articles and slides) given at the URSI scientific days on electromagnetic fields: dosimetry, peoples' exposure, biological and health risks, risk management, and medical uses. 48 presentations are compiled in this document and deal with: 1 - Stochastic dosimetry: variability challenge; 2 - How to estimate the exposure to 50/60 Hz magnetic field in an epidemiological study?; 3 - Joint analysis of population exposure and radio coverage of GSM and UMTS mobile phone networks; 4 - Study of the specific energy absorption rate (SAR) sensitiveness to phone positions near the head for 2 GSM mobile phones; 5 - Statistical Study of SAR under Wireless Channel - Exposure in Indoor Environment; 6 - Uncertainty propagation in numerical dosimetry: how to reduce calculation costs?; 7 - Use of a simplified pregnant woman model for foetus exposure analysis; 8 - SAR estimation using multi-exposure with a mobile phone; 9 - State-of-the-art in experimental dosimetry (RF and pulses); 10 - Mm-waves dosimetry: issues, stakes and actual solutions; 11 - Use of DG-FDTD for a dosimetry calculation in a strongly multi-scale problem: determination of the eye-SAR near a HF/VHF vehicle-borne source; 12 - Dosimetric measurements with a fiber-type electro-optical sensor; 13 - Partial experimental evaluation of basic restrictions in the HF/VHF range; 14 - Repetitive trans-cranial magnetic stimulation Stimulation (rTMS) in psychiatry: present day situation and perspectives; 15 - Medical applications of electric fields; 16 - Measurements for life: new perspectives? 17 - Nano-particles and magnetic stimuli for medical imaging and therapy; 18 - Molecular Insights into electroporation and siRNA electro-transfer through model cell membranes; 19 - State of knowledge on electromagnetic fields hypersensitivity (HS-CEM); 20 - Experimentation methodology: from results to interpretation; 22 - Mm waves - update on biological effects at 40-60 GHz; 23

  13. A comparative analysis on computational methods for fitting an ERGM to biological network data

    Directory of Open Access Journals (Sweden)

    Sudipta Saha

    2015-03-01

    Full Text Available Exponential random graph models (ERGM based on graph theory are useful in studying global biological network structure using its local properties. However, computational methods for fitting such models are sensitive to the type, structure and the number of the local features of a network under study. In this paper, we compared computational methods for fitting an ERGM with local features of different types and structures. Two commonly used methods, such as the Markov Chain Monte Carlo Maximum Likelihood Estimation and the Maximum Pseudo Likelihood Estimation are considered for estimating the coefficients of network attributes. We compared the estimates of observed network to our random simulated network using both methods under ERGM. The motivation was to ascertain the extent to which an observed network would deviate from a randomly simulated network if the physical numbers of attributes were approximately same. Cut-off points of some common attributes of interest for different order of nodes were determined through simulations. We implemented our method to a known regulatory network database of Escherichia coli (E. coli.

  14. Biana: a software framework for compiling biological interactions and analyzing networks.

    Science.gov (United States)

    Garcia-Garcia, Javier; Guney, Emre; Aragues, Ramon; Planas-Iglesias, Joan; Oliva, Baldo

    2010-01-27

    The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

  15. An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks

    Science.gov (United States)

    2014-01-01

    Background Motif mining has always been a hot research topic in bioinformatics. Most of current research on biological networks focuses on exact motif mining. However, due to the inevitable experimental error and noisy data, biological network data represented as the probability model could better reflect the authenticity and biological significance, therefore, it is more biological meaningful to discover probability motif in uncertain biological networks. One of the key steps in probability motif mining is frequent pattern discovery which is usually based on the possible world model having a relatively high computational complexity. Methods In this paper, we present a novel method for detecting frequent probability patterns based on circuit simulation in the uncertain biological networks. First, the partition based efficient search is applied to the non-tree like subgraph mining where the probability of occurrence in random networks is small. Then, an algorithm of probability isomorphic based on circuit simulation is proposed. The probability isomorphic combines the analysis of circuit topology structure with related physical properties of voltage in order to evaluate the probability isomorphism between probability subgraphs. The circuit simulation based probability isomorphic can avoid using traditional possible world model. Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters. Results The experiment results on data sets of the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae show that the proposed method can efficiently discover the frequent probability subgraphs. The discovered subgraphs in our study contain all probability motifs reported in the experiments published in other related papers. Conclusions The algorithm of probability graph isomorphism

  16. MODA: an efficient algorithm for network motif discovery in biological networks.

    Science.gov (United States)

    Omidi, Saeed; Schreiber, Falk; Masoudi-Nejad, Ali

    2009-10-01

    In recent years, interest has been growing in the study of complex networks. Since Erdös and Rényi (1960) proposed their random graph model about 50 years ago, many researchers have investigated and shaped this field. Many indicators have been proposed to assess the global features of networks. Recently, an active research area has developed in studying local features named motifs as the building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding rather large motifs (larger than 8 nodes) by means of current algorithms is impractical as it demands too much computational effort. In this paper, we present a new algorithm (MODA) that incorporates techniques such as a pattern growth approach for extracting larger motifs efficiently. We have tested our algorithm and found it able to identify larger motifs with more than 8 nodes more efficiently than most of the current state-of-the-art motif discovery algorithms. While most of the algorithms rely on induced subgraphs as motifs of the networks, MODA is able to extract both induced and non-induced subgraphs simultaneously. The MODA source code is freely available at: http://LBB.ut.ac.ir/Download/LBBsoft/MODA/

  17. Dosimetry in radiotherapy. V.1

    International Nuclear Information System (INIS)

    1988-01-01

    A series of symposia on dosimetry in medicine and biology have been held by the IAEA in co-operation with WHO. The present symposium was the first one focusing on ''Dosimetry in Radiotherapy''. The papers presented reflected the different steps in the calibration chain such as the calibration standards established by the National Standards Laboratories and the conversion of the reading of calibrated instruments to the desired quantity, i.e. absorbed dose to water at a reference point in the user's beam at the radiotherapy clinic. The programme further examined the procedures necessary for optimization of the treatment of the patient, such as treatment planning methods, dose distribution studies, new techniques of dose measurement, improvements in the physical dose distributions/conformation therapy and special problems involved in total body treatments. Results of quality assurance in radiotherapy were presented from local hospitals as well as from national and international studies. Refs, figs and tabs

  18. A review of active learning approaches to experimental design for uncovering biological networks

    Science.gov (United States)

    2017-01-01

    Various types of biological knowledge describe networks of interactions among elementary entities. For example, transcriptional regulatory networks consist of interactions among proteins and genes. Current knowledge about the exact structure of such networks is highly incomplete, and laboratory experiments that manipulate the entities involved are conducted to test hypotheses about these networks. In recent years, various automated approaches to experiment selection have been proposed. Many of these approaches can be characterized as active machine learning algorithms. Active learning is an iterative process in which a model is learned from data, hypotheses are generated from the model to propose informative experiments, and the experiments yield new data that is used to update the model. This review describes the various models, experiment selection strategies, validation techniques, and successful applications described in the literature; highlights common themes and notable distinctions among methods; and identifies likely directions of future research and open problems in the area. PMID:28570593

  19. Networks In Real Space: Characteristics and Analysis for Biology and Mechanics

    Science.gov (United States)

    Modes, Carl; Magnasco, Marcelo; Katifori, Eleni

    Functional networks embedded in physical space play a crucial role in countless biological and physical systems, from the efficient dissemination of oxygen, blood sugars, and hormonal signals in vascular systems to the complex relaying of informational signals in the brain to the distribution of stress and strain in architecture or static sand piles. Unlike their more-studied abstract cousins, such as the hyperlinked internet, social networks, or economic and financial connections, these networks are both constrained by and intimately connected to the physicality of their real, embedding space. We report on the results of new computational and analytic approaches tailored to these physical networks with particular implications and insights for mammalian organ vasculature.

  20. A Systems’ Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks

    Directory of Open Access Journals (Sweden)

    Xin Lai

    2013-01-01

    Full Text Available MicroRNAs (miRNAs are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. To demonstrate the application of this approach, we adopt it to investigate mechanisms of collective repression on p21 by multiple miRNAs. We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts.

  1. MSD-MAP: A Network-Based Systems Biology Platform for Predicting Disease-Metabolite Links.

    Science.gov (United States)

    Wathieu, Henri; Issa, Naiem T; Mohandoss, Manisha; Byers, Stephen W; Dakshanamurthy, Sivanesan

    2017-01-01

    Cancer-associated metabolites result from cell-wide mechanisms of dysregulation. The field of metabolomics has sought to identify these aberrant metabolites as disease biomarkers, clues to understanding disease mechanisms, or even as therapeutic agents. This study was undertaken to reliably predict metabolites associated with colorectal, esophageal, and prostate cancers. Metabolite and disease biological action networks were compared in a computational platform called MSD-MAP (Multi Scale Disease-Metabolite Association Platform). Using differential gene expression analysis with patient-based RNAseq data from The Cancer Genome Atlas, genes up- or down-regulated in cancer compared to normal tissue were identified. Relational databases were used to map biological entities including pathways, functions, and interacting proteins, to those differential disease genes. Similar relational maps were built for metabolites, stemming from known and in silico predicted metabolite-protein associations. The hypergeometric test was used to find statistically significant relationships between disease and metabolite biological signatures at each tier, and metabolites were assessed for multi-scale association with each cancer. Metabolite networks were also directly associated with various other diseases using a disease functional perturbation database. Our platform recapitulated metabolite-disease links that have been empirically verified in the scientific literature, with network-based mapping of jointly-associated biological activity also matching known disease mechanisms. This was true for colorectal, esophageal, and prostate cancers, using metabolite action networks stemming from both predicted and known functional protein associations. By employing systems biology concepts, MSD-MAP reliably predicted known cancermetabolite links, and may serve as a predictive tool to streamline conventional metabolomic profiling methodologies. Copyright© Bentham Science Publishers; For any

  2. High energy dosimetry

    International Nuclear Information System (INIS)

    Ruhm, W.

    2010-01-01

    Full text: Currently, quantification of doses from high-energy radiation fields is a topical issue. This is so because high-energy neutrons play an important role for radiation exposure of air crew members and personnel outside the shielding of ion therapy facilities. In an effort to study air crew exposure from cosmic radiation in detail, two Bonner Sphere Spectrometers (BSSs) have recently been installed to measure secondary neutrons from cosmic radiation, one at the environmental research station 'Schneefernerhaus' at an altitude of 2650 m on the Zugspitze mountain, Germany, the other at the Koldewey station close to the North Pole on Spitsbergen. Based on the measured neutron fluence distributions and on fluence-to-dose conversion coefficients, mean ambient dose equivalent rate values of 75.0 ± 2.9 nSv/h and 8.7 ± 0.6 nSv/h were obtained for October 2008, respectively. Neutrons with energies above about 20 MeV contribute about 50% to dose, at 2650 m. Ambient dose equivalent rates measured by means of a standard rem counter and an extended rem counter at the Schneefernerhaus confirm this result. In order to study the response of state-of-the-art radiation instrumentation in such a high-energy radiation field, a benchmark exercise that included both measurements in and simulation of the stray neutron radiation field at the high-energy particle accelerator at GSI, Germany, were performed. This CONRAD (COordinated Network for RAdiation Dosimetry) project was funded by the European Commission, and the organizational framework was provided by the European Radiation Dosimetry Group, EURADOS. The Monte Carlo simulations of the radiation field and the experimental determination of the neutron spectra with various Bonner Sphere Spectrometers suggest the neutron fluence distributions to be very similar to those of secondary neutrons from cosmic radiation. The results of this intercomparison exercise in terms of ambient dose equivalent are also discussed

  3. Dosimetry in radionuclide therapy

    International Nuclear Information System (INIS)

    Riccabona, G.

    2001-01-01

    While it is known that therapeutic effects of radionuclides are due to absorbed radiation dose and to radiosensitivity, individual dosimetry in 'Gy' is practiced rarely in clinical Nuclear Medicine but 'doses' are described in 'mCi' or 'MBq', which is only indirectly related to 'Gy' in the target. To estimate 'Gy', the volume of the target, maximum concentration of the radiopharmaceutical in it and residence time should be assessed individually. These parameters can be obtained usually only with difficulty, involving possibly also quantitative SPET or PET, modern imaging techniques (sonography, CT, MRT), substitution of y- or positron emitting radiotracers for β - emitting radiopharmaceuticals as well as whole-body distribution studies. Residence time can be estimated by obtaining data on biological half-life of a comparable tracer and transfer of these data in the physical characteristics of the therapeutic agent. With all these possibilities for gross dosimetry the establishment of a dose-response-relation should be possible. As distribution of the radiopharmaceutical in lesions is frequently inhomogenous and microdosimetric conditions are difficult to assess in vivo as yet, it could be observed since decades that empirically set, sometimes 'fixed' doses (mCi or MBq) can also be successful in many diseases. Detailed dosimetric studies, however, are work- and cost-intensive. Nevertheless, one should be aware at a time when more sophisticated therapeutic possibilities in Nuclear Medicine arise, that we should try to estimate radiation dose (Gy) in our new methods even as differences in individual radiosensitivity cannot be assessed yet and studies to define individual radiosensitivity in lesions should be encouraged. (author)

  4. Thermoluminescence albedo-neutron dosimetry

    International Nuclear Information System (INIS)

    Strand, T.; Storruste, A.

    1986-10-01

    The report discusses neutron detection with respect to dosimetry and compares different thermoluminescent dosimetry materials for neutron dosimetry. Construction and calibration of a thermoluminescence albedo neutron dosemeter, developed by the authors, is described

  5. Biologically-inspired On-chip Learning in Pulsed Neural Networks

    DEFF Research Database (Denmark)

    Lehmann, Torsten; Woodburn, Robin

    1999-01-01

    Self-learning chips to implement many popular ANN (artificial neural network) algorithms are very difficult to design. We explain why this is so and say what lessons previous work teaches us in the design of self-learning systems. We offer a contribution to the "biologically-inspired" approach......, explaining what we mean by this term and providing an example of a robust, self-learning design that can solve simple classical-conditioning tasks, We give details of the design of individual circuits to perform component functions, which can then be combined into a network to solve the task. We argue...

  6. Thermoluminescence in medical dosimetry

    International Nuclear Information System (INIS)

    Rivera, T.

    2011-10-01

    The dosimetry by thermoluminescence (Tl) is applied in the entire world for the dosimetry of ionizing radiations specially to personal and medical dosimetry. This dosimetry method has been very interesting for measures in vivo because the Tl dosimeters have the advantage of being very sensitive in a very small volume and they are also equivalent to tissue and they do not need additional accessories (for example, cable, electrometer, etc.) The main characteristics of the diverse Tl materials to be used in the radiation measures and practical applications are: the Tl curve, the share homogeneity, the signal stability after the irradiation, precision and exactitude, the response in function with the dose and the energy influence. In this work a brief summary of the advances of the radiations dosimetry is presented by means of the thermally stimulated luminescence and its application to the dosimetry in radiotherapy. (Author)

  7. Thin film tritium dosimetry

    Science.gov (United States)

    Moran, Paul R.

    1976-01-01

    The present invention provides a method for tritium dosimetry. A dosimeter comprising a thin film of a material having relatively sensitive RITAC-RITAP dosimetry properties is exposed to radiation from tritium, and after the dosimeter has been removed from the source of the radiation, the low energy electron dose deposited in the thin film is determined by radiation-induced, thermally-activated polarization dosimetry techniques.

  8. Visual analysis of transcriptome data in the context of anatomical structures and biological networks

    Directory of Open Access Journals (Sweden)

    Astrid eJunker

    2012-11-01

    Full Text Available The complexity and temporal as well as spatial resolution of transcriptome datasets is constantly increasing due to extensive technological developments. Here we present methods for advanced visualization and intuitive exploration of transcriptomics data as necessary prerequisites in order to facilitate the gain of biological knowledge. Color-coding of structural images based on the expression level enables a fast visual data analysis in the background of the examined biological system. The network-based exploration of these visualizations allows for comparative analysis of genes with specific transcript patterns and supports the extraction of functional relationships even from large datasets. In order to illustrate the presented methods, the tool HIVE was applied for visualization and exploration of database-retrieved expression data for master regulators of Arabidopsis thaliana flower and seed development in the context of corresponding tissue-specific regulatory networks.

  9. Dosimetry of ionizing radiation

    International Nuclear Information System (INIS)

    Musilek, L.; Seda, J.; Trousil, J.

    1992-01-01

    The publication deals with a major field of ionizing radiation dosimetry, viz., integrating dosimetric methods, which are the basic means of operative dose determination. It is divided into the following sections: physical and chemical effects of ionizing radiation; integrating dosimetric methods for low radiation doses (film dosimetry, nuclear emulsions, thermoluminescence, radiophotoluminescence, solid-state track detectors, integrating ionization dosemeters); dosimetry of high ionizing radiation doses (chemical dosimetric methods, dosemeters based on the coloring effect, activation detectors); additional methods applicable to integrating dosimetry (exoelectron emission, electron spin resonance, lyoluminescence, etc.); and calibration techniques for dosimetric instrumentation. (Z.S.). 422 refs

  10. Neutron spectrometry and dosimetry with neural networks and Bonner spheres: a study to reduce the spheres number; Espectrometria y dosimetria neutronica con redes neuronales y esferas Bonner: un estudio para reducir el numero de esferas

    Energy Technology Data Exchange (ETDEWEB)

    Espinoza G, J. G.; Martinez B, M. R.; Leon P, A. A.; Hernandez P, C. F.; Castaneda M, V. H.; Solis S, L. O.; Castaneda M, R.; Ortiz R, J. M.; Vega C, H. R. [Universidad Autonoma de Zacatecas, Av. Ramon Lopez Velarde 801, Col. Centro, 98000 Zacatecas, Zac. (Mexico); Mendez, R. [Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas, Laboratorio de Patrones Neutronicos, Av. Complutense 22, 28040 Madrid (Spain); Gallego, E. [Universidad Politecnica de Madrid, Departamento de Ingenieria Nuclear, C. Jose Gutierrez Abascal 2, 28006 Madrid (Spain); De Sousa L, M. A. [Centro de Desenvolvimento da Tecnologia Nuclear / CNEN, Av. Pte. Antonio Carlos 6627, Pampulha, 31270-901 Belo Horizonte, MG (Brazil)

    2016-10-15

    For neutron spectrometry and neutron dosimetry, the Bonner spheres spectrometric system has been the most widely used system, however, the number, size and weight of the spheres composing the system, as well as the need to use a reconstruction code and the long periods of time used to carry out the measurements are some of the disadvantages of this system. For the reconstruction of the spectra, different techniques such as artificial neural networks of reverse propagation have been used. The objective of this work was to reduce the number of Bonner spheres and to use counting speeds in a reverse propagation neural network, optimized by means of the robust design methodology, to reconstruct the neutron spectra. For the design of the neural network we used the neutron spectra of the IAEA and the response matrix of the Bonner spheres with {sup 6}LiI(Eu) detector. The performance of the network was compared; using 7 Bonner spheres against other cases where only 2 and one sphere are used. The network topologies were trained 36 times for each case keeping constant the objective error (1E(-3)), the training algorithm was trains cg and the robust design methodology to determine the best network architectures. With these, the best and worst results were compared. The results obtained using 7 spheres were similar to those with the 5-in sphere, however is still in an information analysis stage. (Author)

  11. Convolutional Deep Belief Networks for Single-Cell/Object Tracking in Computational Biology and Computer Vision

    OpenAIRE

    Zhong, Bineng; Pan, Shengnan; Zhang, Hongbo; Wang, Tian; Du, Jixiang; Chen, Duansheng; Cao, Liujuan

    2016-01-01

    In this paper, we propose deep architecture to dynamically learn the most discriminative features from data for both single-cell and object tracking in computational biology and computer vision. Firstly, the discriminative features are automatically learned via a convolutional deep belief network (CDBN). Secondly, we design a simple yet effective method to transfer features learned from CDBNs on the source tasks for generic purpose to the object tracking tasks using only limited amount of tra...

  12. Scientific committee of the IAEA/WHO Network of Secondary Standard Dosimetry Laboratories. Report of the ninth meeting of the SSDL scientific committee, IAEA, Vienna, 13-17 November 2000

    International Nuclear Information System (INIS)

    2001-01-01

    The report of the eighth meeting (held in Oct. 1998) of the Scientific Committee (SSC) of the IAEA/WHO network of Secondary Standard Dosimetry Laboratories (SSDL) was published in the SSDL Newsletter No. 40, January 1999. The ninth meeting was held in Vienna at Agency Headquarters from 13 to 17 November 2000. Opening remarks were made by Mr. S. Groth, Director, Division of Human Health (NAHU), Mr. H. Oestensen (WHO), Co-Secretary of the IAEA/WHO SSDL Network, and Mr. Ahmed Meghzifene, acting Section Head, Dosimetry and Medical Radiation Physics (DMRP). The Agency's DMRP sub-programme provides traceable radiation standards to the majority of developing countries over a wide range of energies and dose levels. External-beam radiation therapy and radiation processing (high dose) have a long history and robust links to international standards. Recently the DMRP has developed projects providing robust links for calibration of mammography X-ray beams, brachytherapy sources, and personnel monitoring programmes at the participating SSDLs. Efforts by the Agency and the WHO over the past 5 years have made significant improvements in the return rate and turn-around time in the postal TLD programme, effectively increasing the availability of Agency standards. Two other high-priority items promulgated by the DMRP are: (i) follow-up of quality audit measurements which fall outside the established action levels, and (ii) transfer of postal TLD programmes to national programmes and establishing and maintaining links between these programmes and the DMRP. The SSC still considers both of these as high priority items, commends the DMRP on their efforts, and encourages them to continue to develop activities in these areas. The SSC wishes to emphasize that radiation dosimetry is a necessary adjunct to many programmes that utilize ionizing radiation at various dose levels. The SSC commends the Agency for their continued support for the programmes sponsored through the Dosimetry and

  13. Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.

    Science.gov (United States)

    Muetze, Tanja; Goenawan, Ivan H; Wiencko, Heather L; Bernal-Llinares, Manuel; Bryan, Kenneth; Lynn, David J

    2016-01-01

    Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest. CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store ( http://apps.cytoscape.org/apps/chat).

  14. Scientific days on electromagnetic fields: from dosimetry to human health - Conference proceedings

    International Nuclear Information System (INIS)

    Wiart, J.; Ghanmi, A.; Picon, O.; Conil, E.; Varsier, N.; Hadjem, A.; Sudret, B.; Magne, I.; Souques, M.; Gaudaire, F.; De Seze, R.; Jawad, O.; Lautru, D.; Dricot, J.M.; Horlin, F.; De Doncker, P.; Drissaoui, A.; Musy, F.; Nicolas, L.; Perrussel, R.; Scorretti, R.; Voyer, D.; Jala, M.; Moulines, E.; Levy-Leduc, C.; Mahfouz, Z.; Gati, A.; Fouad Hanna, V.; Leveque, P.; Arnaud-Cormos, D.; Zhadobov, M.; Jarrige, P.; Gaborit, G.; Kohler, S.; Ticaud, N.; Duvillaret, L.; Guelilia, Z.; Loison, R.; Gillard, R.; Laisne, A.; Favet, D.; Benadhira, R.; Mir, L.; Nadi, M.; Kourtiche, D.; Gazeau, F.; Wilhelm, C.; Delemotte, L.; Breton, M.; Tarek, M.; Marc-Vergnes, J.P.; Yardin, C.; Perrin, A.; Le Drean, Y.; Sauleau, R.; Lambrozo, J.; Selmaoui, B.; Ghosn, R.; Thuroczy, G.; Villegier, A.S.; Loos, N.; Brenet-Dufour, V.; Liabeuf, S.; Bach, V.; Moretti, D.; Lewis, N.; Garenne, A.; Poulletier De Gannes, F.; Haro, E.; Lagroye, I.; Bornat, Y.; Boutaib, Y.; Saighi, S.; Renaud, S.; Veyre, B.; Schuz, J.; Deltour, I.; Van Deventer, E.; Vecchia, P.; Merckel, O.; Bellaouel, A.; Demaret, P.; Donati, P.; Jovanovic, D.; Chauvin, S.; Desreumaux, J.P.; Fouquet, L.; Picard, D.; Massardier-Pilonchery, A.; Hours, M.; Bergeret, A.; Person, C.; Toutain, Y.; Butet, R.; Berrahma, K.; Balderelli, I.; Stelmaszyk, V.; Cretallaz, C.; Lamproglou, I.; Amourette, C.; Diserbo, M.; Fauquette, W.; Martigne, P.; Collin, A.; Lagroye, I.; Ait Aissa, S.; Hurtier, A.; Taxile, M.; Le Montagner, L.; Athane, A.; Duleu, S.; Percherancier, Y.; Geffard, M.; Ruffie, G.; Billaudel, B.; Veyret, B.; Pelletier, A.; Delanaud, S.; Libert, J.P.; Schunck, T.; Bieth, F.; Soubere Mahamoud, Y.; Le Quement, C.; Ferrand, G.; Le Guevel, R.; Carton, P.H.; Luong, M.; Tanvir, S.; Selmaoui, B.; Silva Pires-Antonietti, V.; Sonnet, P.; Pulvin, S.; Kuster, O.; Tetelin, C.

    2012-04-01

    This document brings together the available presentations (articles and slides) given at the URSI scientific days on electromagnetic fields: dosimetry, peoples' exposure, biological and health risks, risk management, and medical uses. 48 presentations are compiled in this document and deal with: 1 - Stochastic dosimetry: variability challenge; 2 - How to estimate the exposure to 50/60 Hz magnetic field in an epidemiological study?; 3 - Joint analysis of population exposure and radio coverage of GSM and UMTS mobile phone networks; 4 - Study of the specific energy absorption rate (SAR) sensitiveness to phone positions near the head for 2 GSM mobile phones; 5 - Statistical Study of SAR under Wireless Channel - Exposure in Indoor Environment; 6 - Uncertainty propagation in numerical dosimetry: how to reduce calculation costs?; 7 - Use of a simplified pregnant woman model for foetus exposure analysis; 8 - SAR estimation using multi-exposure with a mobile phone; 9 - State-of-the-art in experimental dosimetry (RF and pulses); 10 - Mm-waves dosimetry: issues, stakes and actual solutions; 11 - Use of DG-FDTD for a dosimetry calculation in a strongly multi-scale problem: determination of the eye-SAR near a HF/VHF vehicle-borne source; 12 - Dosimetric measurements with a fiber-type electro-optical sensor; 13 - Partial experimental evaluation of basic restrictions in the HF/VHF range; 14 - Repetitive trans-cranial magnetic stimulation Stimulation (rTMS) in psychiatry: present day situation and perspectives; 15 - Medical applications of electric fields; 16 - Measurements for life: new perspectives? 17 - Nano-particles and magnetic stimuli for medical imaging and therapy; 18 - Molecular Insights into electroporation and siRNA electro-transfer through model cell membranes; 19 - State of knowledge on electromagnetic fields hypersensitivity (HS-CEM); 20 - Experimentation methodology: from results to interpretation; 22 - Mm waves - update on biological effects at 40-60 GHz; 23

  15. Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays

    Directory of Open Access Journals (Sweden)

    Wu Xiaogang

    2012-06-01

    Full Text Available In many cases, crucial genes show relatively slight changes between groups of samples (e.g. normal vs. disease, and many genes selected from microarray differential analysis by measuring the expression level statistically are also poorly annotated and lack of biological significance. In this paper, we present an innovative approach - network expansion and pathway enrichment analysis (NEPEA for integrative microarray analysis. We assume that organized knowledge will help microarray data analysis in significant ways, and the organized knowledge could be represented as molecular interaction networks or biological pathways. Based on this hypothesis, we develop the NEPEA framework based on network expansion from the human annotated and predicted protein interaction (HAPPI database, and pathway enrichment from the human pathway database (HPD. We use a recently-published microarray dataset (GSE24215 related to insulin resistance and type 2 diabetes (T2D as case study, since this study provided a thorough experimental validation for both genes and pathways identified computationally from classical microarray analysis and pathway analysis. We perform our NEPEA analysis for this dataset based on the results from the classical microarray analysis to identify biologically significant genes and pathways. Our findings are not only consistent with the original findings mostly, but also obtained more supports from other literatures.

  16. A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks

    Science.gov (United States)

    Hruz, Tomas; Lucas, Christoph; Laule, Oliver; Zimmermann, Philip

    2013-01-01

    Visualization of large complex networks has become an indispensable part of systems biology, where organisms need to be considered as one complex system. The visualization of the corresponding network is challenging due to the size and density of edges. In many cases, the use of standard visualization algorithms can lead to high running times and poorly readable visualizations due to many edge crossings. We suggest an approach that analyzes the structure of the graph first and then generates a new graph which contains specific semantic symbols for regular substructures like dense clusters. We propose a multilevel gamma-clustering layout visualization algorithm (MLGA) which proceeds in three subsequent steps: (i) a multilevel γ-clustering is used to identify the structure of the underlying network, (ii) the network is transformed to a tree, and (iii) finally, the resulting tree which shows the network structure is drawn using a variation of a force-directed algorithm. The algorithm has a potential to visualize very large networks because it uses modern clustering heuristics which are optimized for large graphs. Moreover, most of the edges are removed from the visual representation which allows keeping the overview over complex graphs with dense subgraphs. PMID:23864855

  17. Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis

    Science.gov (United States)

    Scott, RE; Ghule, PN; Stein, JL; Stein, GS

    2015-01-01

    The early stages of carcinogenesis are linked to defects in the cell cycle. A series of cell cycle checkpoints are involved in this process. The G1/S checkpoint that serves to integrate the control of cell proliferation and differentiation is linked to carcinogenesis and the mitotic spindle checkpoint with the development of chromosomal instability. This paper presents the outcome of systems biology studies designed to evaluate if networks of covariate cell cycle gene transcripts exist in proliferative mammalian tissues including mice, rats and humans. The GeneNetwork website that contains numerous gene expression datasets from different species, sexes and tissues represents the foundational resource for these studies (www.genenetwork.org). In addition, WebGestalt, a gene ontology tool, facilitated the identification of expression networks of genes that co-vary with key cell cycle targets, especially Cdc20 and Plk1 (www.bioinfo.vanderbilt.edu/webgestalt). Cell cycle expression networks of such covariate mRNAs exist in multiple proliferative tissues including liver, lung, pituitary, adipose and lymphoid tissues among others but not in brain or retina that have low proliferative potential. Sixty-three covariate cell cycle gene transcripts (mRNAs) compose the average cell cycle network with p = e−13 to e−36. Cell cycle expression networks show species, sex and tissue variability and they are enriched in mRNA transcripts associated with mitosis many of which are associated with chromosomal instability. PMID:25808367

  18. Recurrent Convolutional Neural Networks: A Better Model of Biological Object Recognition.

    Science.gov (United States)

    Spoerer, Courtney J; McClure, Patrick; Kriegeskorte, Nikolaus

    2017-01-01

    Feedforward neural networks provide the dominant model of how the brain performs visual object recognition. However, these networks lack the lateral and feedback connections, and the resulting recurrent neuronal dynamics, of the ventral visual pathway in the human and non-human primate brain. Here we investigate recurrent convolutional neural networks with bottom-up (B), lateral (L), and top-down (T) connections. Combining these types of connections yields four architectures (B, BT, BL, and BLT), which we systematically test and compare. We hypothesized that recurrent dynamics might improve recognition performance in the challenging scenario of partial occlusion. We introduce two novel occluded object recognition tasks to test the efficacy of the models, digit clutter (where multiple target digits occlude one another) and digit debris (where target digits are occluded by digit fragments). We find that recurrent neural networks outperform feedforward control models (approximately matched in parametric complexity) at recognizing objects, both in the absence of occlusion and in all occlusion conditions. Recurrent networks were also found to be more robust to the inclusion of additive Gaussian noise. Recurrent neural networks are better in two respects: (1) they are more neurobiologically realistic than their feedforward counterparts; (2) they are better in terms of their ability to recognize objects, especially under challenging conditions. This work shows that computer vision can benefit from using recurrent convolutional architectures and suggests that the ubiquitous recurrent connections in biological brains are essential for task performance.

  19. Cellular dosimetry

    International Nuclear Information System (INIS)

    Humm, J.L.; Chin, L.M.

    1989-01-01

    Radiation dose is a useful predictive parameter for describing radiation toxicity in conventional radiotherapy. Traditionally, in vitro radiation biology dose-effect relations are expressed in the form of cell survival curves, a semilog plot of cell survival versus dose. However, the characteristic linear or linear quadratic survival curve shape, for high- and low-LET radiations respectively, is only strictly valid when the radiation dose is uniform across the entire target population. With an external beam of 60 Co gamma rays or x-rays, a uniform field may be readily achievable. When radionuclides are incorporated into a cell milieu, several new problems emerge which can result in a departure from uniformity in energy deposition throughout a cell population. This nonuniformity can have very important consequences for the shape of the survival curve. Cases in which perturbations of source uniformity may arise include: 1. Elemental sources may equilibrate in the cell medium with partition coefficients between the extracellular, cytosol, and nuclear compartments. The effect of preferential cell internalization or binding to cell membrane of some radionuclides can increase or decrease the slope of the survival curve. 2. Radionuclides bound to antibodies, hormones, metabolite precursors, etc., may result in a source localization pattern characteristic of the carrier agent, i.e., the sources may bind to cell surface receptors or antigens, be internalized, bind to secreted antigen concentrated around a fraction of the cell population, or become directly incorporated into the cell DNA. We propose to relate the distribution of energy deposition in cell nuclei to biological correlates of cellular inactivation. The probability of each cell's survival is weighted by its individual radiation burden, and the summation of these probabilities for the cell population can be used to predict the number or fraction of cell survivors

  20. From systems biology to photosynthesis and whole-plant physiology: a conceptual model for integrating multi-scale networks.

    Science.gov (United States)

    Weston, David J; Hanson, Paul J; Norby, Richard J; Tuskan, Gerald A; Wullschleger, Stan D

    2012-02-01

    Network analysis is now a common statistical tool for molecular biologists. Network algorithms are readily used to model gene, protein and metabolic correlations providing insight into pathways driving biological phenomenon. One output from such an analysis is a candidate gene list that can be responsible, in part, for the biological process of interest. The question remains, however, as to whether molecular network analysis can be used to inform process models at higher levels of biological organization. In our previous work, transcriptional networks derived from three plant species were constructed, interrogated for orthology and then correlated with photosynthetic inhibition at elevated temperature. One unique aspect of that study was the link from co-expression networks to net photosynthesis. In this addendum, we propose a conceptual model where traditional network analysis can be linked to whole-plant models thereby informing predictions on key processes such as photosynthesis, nutrient uptake and assimilation, and C partitioning.

  1. EPR dosimetry - present and future

    International Nuclear Information System (INIS)

    Regulla, D.F.

    1999-01-01

    In the past, IAEA has played a central role in stipulating research and development in EPR high-dose standardisation as well as co-ordinating and organising international dose intercomparison programs, within the Member States of the United Nations from the mid-seventies till today. The future tasks of EPR dosimetry seem to tend towards different subjects such as biomarkers, biological radiation effects, post-accident dose reconstruction in the environment, and retrospective human dosimetry. The latter may be considered a promising tool for epidemiology on the way to re-define radiation risk of man for chronicle radiation exposures, based on e.g. South Ural civil population and radiation workers. There are on-going international activities in the field of standardising high-level dosimetry by the American Standards on Testing and Materials (ASTM), and the International Organisation of Standards (ISO) as well as those of the International Commission on Radiation Units and Measurements (ICRU) considering the establishment of relevant recommendations concerning industrial radiation processing, but also human dose reconstruction. (author)

  2. EPR Dosimetry - Present and Future

    Energy Technology Data Exchange (ETDEWEB)

    Regulla, D.F. [GSF - National Research Centre for Environment and Health, Institute of Radiation Protection, 85764 Neuherberg (Germany)

    1999-07-01

    In the past, IAEA has played a central role in stipulating research and development in EPR high-dose standardisation as well as in coordinating and organising international dose intercomparison programs, within the Member States of the United Nations from the mid-seventies till today. The future tasks of EPR dosimetry seem to tend towards different subjects such as bio markers, biological radiation effects, post-accident dose reconstruction in the environment, and retrospective human dosimetry. The latter may be considered a promising tool for epidemiology on the way to re-define radiation risk of man for chronicle radiation exposures, based on e.g. South Ural civil population and radiation workers. There are on-going international activities in the field of standardising high-level dosimetry by the American Standards on Testing and Materials (Astm), and by the International Organisation of Standards (ISO). The International Commission on Radiation Units and Measurements (ICRU) is considering the establishment of relevant recommendations concerning industrial radiation processing, but also human dose reconstruction. (Author)

  3. EPR Dosimetry - Present and Future

    International Nuclear Information System (INIS)

    Regulla, D.F.

    1999-01-01

    In the past, IAEA has played a central role in stipulating research and development in EPR high-dose standardisation as well as in coordinating and organising international dose intercomparison programs, within the Member States of the United Nations from the mid-seventies till today. The future tasks of EPR dosimetry seem to tend towards different subjects such as bio markers, biological radiation effects, post-accident dose reconstruction in the environment, and retrospective human dosimetry. The latter may be considered a promising tool for epidemiology on the way to re-define radiation risk of man for chronicle radiation exposures, based on e.g. South Ural civil population and radiation workers. There are on-going international activities in the field of standardising high-level dosimetry by the American Standards on Testing and Materials (Astm), and by the International Organisation of Standards (ISO). The International Commission on Radiation Units and Measurements (ICRU) is considering the establishment of relevant recommendations concerning industrial radiation processing, but also human dose reconstruction. (Author)

  4. Iterative Systems Biology for Medicine – time for advancing from network signature to mechanistic equations

    KAUST Repository

    Gomez-Cabrero, David

    2017-05-09

    The rise and growth of Systems Biology following the sequencing of the human genome has been astounding. Early on, an iterative wet-dry methodology was formulated which turned out as a successful approach in deciphering biological complexity. Such type of analysis effectively identified and associated molecular network signatures operative in biological processes across different systems. Yet, it has proven difficult to distinguish between causes and consequences, thus making it challenging to attack medical questions where we require precise causative drug targets and disease mechanisms beyond a web of associated markers. Here we review principal advances with regard to identification of structure, dynamics, control, and design of biological systems, following the structure in the visionary review from 2002 by Dr. Kitano. Yet, here we find that the underlying challenge of finding the governing mechanistic system equations enabling precision medicine remains open thus rendering clinical translation of systems biology arduous. However, stunning advances in raw computational power, generation of high-precision multi-faceted biological data, combined with powerful algorithms hold promise to set the stage for data-driven identification of equations implicating a fundamental understanding of living systems during health and disease.

  5. Biologics or tofacitinib for people with rheumatoid arthritis unsuccessfully treated with biologics: a systematic review and network meta-analysis.

    Science.gov (United States)

    Singh, Jasvinder A; Hossain, Alomgir; Tanjong Ghogomu, Elizabeth; Mudano, Amy S; Maxwell, Lara J; Buchbinder, Rachelle; Lopez-Olivo, Maria Angeles; Suarez-Almazor, Maria E; Tugwell, Peter; Wells, George A

    2017-03-10

    Biologic disease-modifying anti-rheumatic drugs (DMARDs: referred to as biologics) are effective in treating rheumatoid arthritis (RA), however there are few head-to-head comparison studies. Our systematic review, standard meta-analysis and network meta-analysis (NMA) updates the 2009 Cochrane overview, 'Biologics for rheumatoid arthritis (RA)' and adds new data. This review is focused on biologic or tofacitinib therapy in people with RA who had previously been treated unsuccessfully with biologics. To compare the benefits and harms of biologics (abatacept, adalimumab, anakinra, certolizumab pegol, etanercept, golimumab, infliximab, rituximab, tocilizumab) and small molecule tofacitinib versus comparator (placebo or methotrexate (MTX)/other DMARDs) in people with RA, previously unsuccessfully treated with biologics. On 22 June 2015 we searched for randomized controlled trials (RCTs) in CENTRAL, MEDLINE, and Embase; and trials registries (WHO trials register, Clinicaltrials.gov). We carried out article selection, data extraction, and risk of bias and GRADE assessments in duplicate. We calculated direct estimates with 95% confidence intervals (CI) using standard meta-analysis. We used a Bayesian mixed treatment comparison (MTC) approach for NMA estimates with 95% credible intervals (CrI). We converted odds ratios (OR) to risk ratios (RR) for ease of understanding. We have also presented results in absolute measures as risk difference (RD) and number needed to treat for an additional beneficial outcome (NNTB). Outcomes measured included four benefits (ACR50, function measured by Health Assessment Questionnaire (HAQ) score, remission defined as DAS tofacitinib (399 participants). The majority of the trials (10/12) lasted less than 12 months.We judged 33% of the studies at low risk of bias for allocation sequence generation, allocation concealment and blinding, 25% had low risk of bias for attrition, 92% were at unclear risk for selective reporting; and 92% had low risk

  6. Biologically plausible learning in neural networks: a lesson from bacterial chemotaxis.

    Science.gov (United States)

    Shimansky, Yury P

    2009-12-01

    Learning processes in the brain are usually associated with plastic changes made to optimize the strength of connections between neurons. Although many details related to biophysical mechanisms of synaptic plasticity have been discovered, it is unclear how the concurrent performance of adaptive modifications in a huge number of spatial locations is organized to minimize a given objective function. Since direct experimental observation of even a relatively small subset of such changes is not feasible, computational modeling is an indispensable investigation tool for solving this problem. However, the conventional method of error back-propagation (EBP) employed for optimizing synaptic weights in artificial neural networks is not biologically plausible. This study based on computational experiments demonstrated that such optimization can be performed rather efficiently using the same general method that bacteria employ for moving closer to an attractant or away from a repellent. With regard to neural network optimization, this method consists of regulating the probability of an abrupt change in the direction of synaptic weight modification according to the temporal gradient of the objective function. Neural networks utilizing this method (regulation of modification probability, RMP) can be viewed as analogous to swimming in the multidimensional space of their parameters in the flow of biochemical agents carrying information about the optimality criterion. The efficiency of RMP is comparable to that of EBP, while RMP has several important advantages. Since the biological plausibility of RMP is beyond a reasonable doubt, the RMP concept provides a constructive framework for the experimental analysis of learning in natural neural networks.

  7. Double network bacterial cellulose hydrogel to build a biology-device interface

    Science.gov (United States)

    Shi, Zhijun; Li, Ying; Chen, Xiuli; Han, Hongwei; Yang, Guang

    2013-12-01

    Establishing a biology-device interface might enable the interaction between microelectronics and biotechnology. In this study, electroactive hydrogels have been produced using bacterial cellulose (BC) and conducting polymer (CP) deposited on the BC hydrogel surface to cover the BC fibers. The structures of these composites thus have double networks, one of which is a layer of electroactive hydrogels combined with BC and CP. The electroconductivity provides the composites with capabilities for voltage and current response, and the BC hydrogel layer provides good biocompatibility, biodegradability, bioadhesion and mass transport properties. Such a system might allow selective biological functions such as molecular recognition and specific catalysis and also for probing the detailed genetic and molecular mechanisms of life. A BC-CP composite hydrogel could then lead to a biology-device interface. Cyclic voltammetry and electrochemical impedance spectroscopy (EIS) are used here to study the composite hydrogels' electroactive property. BC-PAni and BC-PPy respond to voltage changes. This provides a mechanism to amplify electrochemical signals for analysis or detection. BC hydrogels were found to be able to support the growth, spreading and migration of human normal skin fibroblasts without causing any cytotoxic effect on the cells in the cell culture. These double network BC-CP hydrogels are biphasic Janus hydrogels which integrate electroactivity with biocompatibility, and might provide a biology-device interface to produce implantable devices for personalized and regenerative medicine.

  8. Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data

    Directory of Open Access Journals (Sweden)

    Gao Shouguo

    2011-08-01

    Full Text Available Abstract Background Bayesian Network (BN is a powerful approach to reconstructing genetic regulatory networks from gene expression data. However, expression data by itself suffers from high noise and lack of power. Incorporating prior biological knowledge can improve the performance. As each type of prior knowledge on its own may be incomplete or limited by quality issues, integrating multiple sources of prior knowledge to utilize their consensus is desirable. Results We introduce a new method to incorporate the quantitative information from multiple sources of prior knowledge. It first uses the Naïve Bayesian classifier to assess the likelihood of functional linkage between gene pairs based on prior knowledge. In this study we included cocitation in PubMed and schematic similarity in Gene Ontology annotation. A candidate network edge reservoir is then created in which the copy number of each edge is proportional to the estimated likelihood of linkage between the two corresponding genes. In network simulation the Markov Chain Monte Carlo sampling algorithm is adopted, and samples from this reservoir at each iteration to generate new candidate networks. We evaluated the new algorithm using both simulated and real gene expression data including that from a yeast cell cycle and a mouse pancreas development/growth study. Incorporating prior knowledge led to a ~2 fold increase in the number of known transcription regulations recovered, without significant change in false positive rate. In contrast, without the prior knowledge BN modeling is not always better than a random selection, demonstrating the necessity in network modeling to supplement the gene expression data with additional information. Conclusion our new development provides a statistical means to utilize the quantitative information in prior biological knowledge in the BN modeling of gene expression data, which significantly improves the performance.

  9. Content-rich biological network constructed by mining PubMed abstracts

    Directory of Open Access Journals (Sweden)

    Sharp Burt M

    2004-10-01

    Full Text Available Abstract Background The integration of the rapidly expanding corpus of information about the genome, transcriptome, and proteome, engendered by powerful technological advances, such as microarrays, and the availability of genomic sequence from multiple species, challenges the grasp and comprehension of the scientific community. Despite the existence of text-mining methods that identify biological relationships based on the textual co-occurrence of gene/protein terms or similarities in abstract texts, knowledge of the underlying molecular connections on a large scale, which is prerequisite to understanding novel biological processes, lags far behind the accumulation of data. While computationally efficient, the co-occurrence-based approaches fail to characterize (e.g., inhibition or stimulation, directionality biological interactions. Programs with natural language processing (NLP capability have been created to address these limitations, however, they are in general not readily accessible to the public. Results We present a NLP-based text-mining approach, Chilibot, which constructs content-rich relationship networks among biological concepts, genes, proteins, or drugs. Amongst its features, suggestions for new hypotheses can be generated. Lastly, we provide evidence that the connectivity of molecular networks extracted from the biological literature follows the power-law distribution, indicating scale-free topologies consistent with the results of previous experimental analyses. Conclusions Chilibot distills scientific relationships from knowledge available throughout a wide range of biological domains and presents these in a content-rich graphical format, thus integrating general biomedical knowledge with the specialized knowledge and interests of the user. Chilibot http://www.chilibot.net can be accessed free of charge to academic users.

  10. Architecture and biological applications of artificial neural networks: a tuberculosis perspective.

    Science.gov (United States)

    Darsey, Jerry A; Griffin, William O; Joginipelli, Sravanthi; Melapu, Venkata Kiran

    2015-01-01

    Advancement of science and technology has prompted researchers to develop new intelligent systems that can solve a variety of problems such as pattern recognition, prediction, and optimization. The ability of the human brain to learn in a fashion that tolerates noise and error has attracted many researchers and provided the starting point for the development of artificial neural networks: the intelligent systems. Intelligent systems can acclimatize to the environment or data and can maximize the chances of success or improve the efficiency of a search. Due to massive parallelism with large numbers of interconnected processers and their ability to learn from the data, neural networks can solve a variety of challenging computational problems. Neural networks have the ability to derive meaning from complicated and imprecise data; they are used in detecting patterns, and trends that are too complex for humans, or other computer systems. Solutions to the toughest problems will not be found through one narrow specialization; therefore we need to combine interdisciplinary approaches to discover the solutions to a variety of problems. Many researchers in different disciplines such as medicine, bioinformatics, molecular biology, and pharmacology have successfully applied artificial neural networks. This chapter helps the reader in understanding the basics of artificial neural networks, their applications, and methodology; it also outlines the network learning process and architecture. We present a brief outline of the application of neural networks to medical diagnosis, drug discovery, gene identification, and protein structure prediction. We conclude with a summary of the results from our study on tuberculosis data using neural networks, in diagnosing active tuberculosis, and predicting chronic vs. infiltrative forms of tuberculosis.

  11. Radiochromic film dosimetry

    International Nuclear Information System (INIS)

    Xu Zhiyong

    2002-01-01

    Radiochromic film dosimetry was developed to measure ionization irradiation dose for industry and medicine. At this time, there are no comprehensive guideline on the medical application, calibration method and densitometer system for medicine. The review gives update on Radiochromic film dosimetry used for medicine, including principles, film model and material, characteristics, calibration method, scanning densitometer system and medical application

  12. Nuclear accident dosimetry

    International Nuclear Information System (INIS)

    1982-01-01

    The film presents statistical data on criticality accidents. It outlines past IAEA activities on criticality accident dosimetry and the technical documents that resulted from this work. The film furthermore illustrates an international comparison study on nuclear accident dosimetry conducted at the Atomic Energy Research Establishment, Harwell, United Kingdom

  13. Personal dosimetry in Kazakhstan

    International Nuclear Information System (INIS)

    Khvoshnyanskaya, I.R.; Vdovichenko, V.G.; Lozbin, A.Yu.

    2003-01-01

    KATEP-AE Radiation Laboratory is the first organization in Kazakhstan officially licensed by the Kazakhstan Atomic Energy Committee to provide individual dosimetry services. The Laboratory was established according to the international standards. Nowadays it is the largest company providing personal dosimetry services in the Republic of Kazakhstan. (author)

  14. Nuclear accident dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1983-12-31

    The film presents statistical data on criticality accidents. It outlines past IAEA activities on criticality accident dosimetry and the technical documents that resulted from this work. The film furthermore illustrates an international comparison study on nuclear accident dosimetry conducted at the Atomic Energy Research Establishment, Harwell, United Kingdom

  15. Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks.

    Science.gov (United States)

    Kastrup, Christian J; Runyon, Matthew K; Lucchetta, Elena M; Price, Jessica M; Ismagilov, Rustem F

    2008-04-01

    Understanding the spatial dynamics of biochemical networks is both fundamentally important for understanding life at the systems level and also has practical implications for medicine, engineering, biology, and chemistry. Studies at the level of individual reactions provide essential information about the function, interactions, and localization of individual molecular species and reactions in a network. However, analyzing the spatial dynamics of complex biochemical networks at this level is difficult. Biochemical networks are nonequilibrium systems containing dozens to hundreds of reactions with nonlinear and time-dependent interactions, and these interactions are influenced by diffusion, flow, and the relative values of state-dependent kinetic parameters. To achieve an overall understanding of the spatial dynamics of a network and the global mechanisms that drive its function, networks must be analyzed as a whole, where all of the components and influential parameters of a network are simultaneously considered. Here, we describe chemical concepts and microfluidic tools developed for network-level investigations of the spatial dynamics of these networks. Modular approaches can be used to simplify these networks by separating them into modules, and simple experimental or computational models can be created by replacing each module with a single reaction. Microfluidics can be used to implement these models as well as to analyze and perturb the complex network itself with spatial control on the micrometer scale. We also describe the application of these network-level approaches to elucidate the mechanisms governing the spatial dynamics of two networkshemostasis (blood clotting) and early patterning of the Drosophila embryo. To investigate the dynamics of the complex network of hemostasis, we simplified the network by using a modular mechanism and created a chemical model based on this mechanism by using microfluidics. Then, we used the mechanism and the model to

  16. Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Milenković, Tijana

    2017-01-05

    Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments. Here, we survey prominent and recent computational approaches of each network alignment type and discuss their (dis)advantages. Then, as it was recently shown that the two approach types are complementary, in the sense that they capture different slices of cellular functioning, we discuss the need to reconcile the two network alignment types and present a recent first step in this direction. We conclude with some open research problems on this topic and comment on the usefulness of network alignment in other domains besides computational biology. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  17. 100 years of solid state dosimetry and radiation protection dosimetry

    International Nuclear Information System (INIS)

    Bartlett, David T.

    2008-01-01

    The use of solid state detectors in radiation dosimetry has passed its 100th anniversary. The major applications of these detectors in radiation dosimetry have been in personal dosimetry, retrospective dosimetry, dating, medical dosimetry, the characterization of radiation fields, and also in microdosimetry and radiobiology research. In this introductory paper for the 15th International Conference, I shall speak of the history of solid state dosimetry and of the radiation measurement quantities that developed at the same time, mention some landmark developments in detectors and applications, speak a bit more about dosimetry and measurement quantities, and briefly look at the past and future

  18. Dosimetry for radiation processing

    International Nuclear Information System (INIS)

    McLaughlin, W.L.; Boyd, A.W.; Chadwick, K.H.; McDonald, J.C.; Miller, A.

    1989-01-01

    Radiation processing is a relatively young industry with broad applications and considerable commercial success. Dosimetry provides an independent and effective way of developing and controlling many industrial processes. In the sterilization of medical devices and in food irradiation, where the radiation treatment impacts directly on public health, the measurements of dose provide the official means of regulating and approving its use. In this respect, dosimetry provides the operator with a means of characterizing the facility, of proving that products are treated within acceptable dose limits and of controlling the routine operation. This book presents an up-to-date review of the theory, data and measurement techniques for radiation processing dosimetry in a practical and useful way. It is hoped that this book will lead to improved measurement procedures, more accurate and precise dosimetry and a greater appreciation of the necessity of dosimetry for radiation processing. (author)

  19. Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

    Science.gov (United States)

    Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

    2016-02-01

    The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

  20. Quantitative Evaluation of Biologic Therapy Options for Psoriasis: A Systematic Review and Network Meta-Analysis.

    Science.gov (United States)

    Jabbar-Lopez, Zarif K; Yiu, Zenas Z N; Ward, Victoria; Exton, Lesley S; Mohd Mustapa, M Firouz; Samarasekera, Eleanor; Burden, A David; Murphy, Ruth; Owen, Caroline M; Parslew, Richard; Venning, Vanessa; Warren, Richard B; Smith, Catherine H

    2017-08-01

    Multiple biologic treatments are licensed for psoriasis. The lack of head-to-head randomized controlled trials makes choosing between them difficult for patients, clinicians, and guideline developers. To establish their relative efficacy and tolerability, we searched MEDLINE, PubMed, Embase, and Cochrane for randomized controlled trials of licensed biologic treatments for skin psoriasis. We performed a network meta-analysis to identify direct and indirect evidence comparing biologics with one another, methotrexate, or placebo. We combined this with hierarchical cluster analysis to consider multiple outcomes related to efficacy and tolerability in combination for each treatment. Study quality, heterogeneity, and inconsistency were evaluated. Direct comparisons from 41 randomized controlled trials (20,561 participants) were included. All included biologics were efficacious compared with placebo or methotrexate at 3-4 months. Overall, cluster analysis showed adalimumab, secukinumab, and ustekinumab were comparable in terms of high efficacy and tolerability. Ixekizumab and infliximab were differentiated by very high efficacy but poorer tolerability. The lack of longer term controlled data limited our analysis to short-term outcomes. Trial performance may not equate to real-world performance, and so results need to be considered alongside real-world, long-term safety and effectiveness data. These data suggest that it is possible to discriminate between biologics to inform clinical practice and decision making (PROSPERO 2015:CRD42015017538). Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  1. Cellular dosimetry in nuclear medicine imaging: training

    International Nuclear Information System (INIS)

    Gardin, I.; Faraggi, M.; Stievenart, J.L.; Le Guludec, D.; Bok, B.

    1998-01-01

    The radionuclides used in nuclear medicine imaging emit not only diagnostically useful photons, but also energy electron emissions, responsible for dose heterogeneity at the cellular level. The mean dose delivered to the cell nucleus by electron emissions of 99m Tc, 123 I, 111 In, 67 Ga, and 201 Tl, has been calculated, for the cell nucleus, a cytoplasmic and a cell membrane distribution of radioactivity. This model takes into account both the self-dose which results from the radionuclide located in the target cell, and the cross-dose, which comes from the surrounding cells. The results obtained by cellular dosimetry (D cel ) have been compared with those obtained with conventional dosimetry (D conv ), by assuming the same amount of radioactivity per cell. Cellular dosimetry shows, for a cytoplasmic and a cell membrane distributions of radioactivity, that the main contribution to the dose to the cell nucleus, comes from the surrounding cells. On the other hand, for a cell nucleus distribution of radioactivity, the self-dose is not negligible and may be the main contribution. The comparison between cellular and conventional dosimetry shows that D cel /D conv ratio ranges from 0.61 and O.89, in case of a cytoplasmic and a cell membrane distributions of radioactivity, depending on the radionuclide and cell dimensions. Thus, conventional dosimetry slightly overestimates the mean dose to the cell nucleus. On the other hand, D cel /D conv ranges from 1.1 to 75, in case of a cell nucleus distribution of radioactivity. Conventional dosimetry may strongly underestimates the absorbed dose to the nucleus, when radioactivity is located in the nucleus. The study indicates that in nuclear medicine imaging, cellular dosimetry may lead to a better understanding of biological effects of radiopharmaceuticals. (authors)

  2. Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer

    Directory of Open Access Journals (Sweden)

    Samra Khalid

    2016-10-01

    Full Text Available Background Breast cancer (BC is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s. It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER-α associated Biological Regulatory Network (BRN for a small part of complex events that leads to BC metastasis. Methods A discrete model was constructed using the kinetic logic formalism and its set of logical parameters were obtained using the model checking technique implemented in the SMBioNet software which is consistent with biological observations. The discrete model was further enriched with continuous dynamics by converting it into an equivalent Petri Net (PN to analyze the logical parameters of the involved entities. Results In-silico based discrete and continuous modeling of ER-α associated signaling network involved in BC provides information about behaviors and gene-gene interaction in detail. The dynamics of discrete model revealed, imperative behaviors represented as cyclic paths and trajectories leading to pathogenic states such as metastasis. Results suggest that the increased expressions of receptors ER-α, IGF-1R and EGFR slow down the activity of tumor suppressor genes (TSGs such as BRCA1, p53 and Mdm2 which can lead to metastasis. Therefore, IGF-1R and EGFR are considered as important inhibitory targets to control the metastasis in BC. Conclusion The in-silico approaches allow us to increase our understanding of the functional properties of living organisms. It opens new avenues of investigations of multiple inhibitory targets (ER-α, IGF-1R and EGFR for wet lab experiments as well as provided valuable insights in the treatment of cancers

  3. Role of secondary standard dosimetry laboratory in radiation protection program

    International Nuclear Information System (INIS)

    Rahman, Sohaila; Ali, Noriah Mohd.

    2008-01-01

    Full text: The radiation dosimetry program is an important element of operational radiation protection. Dosimetry data enable workers and radiation protection professionals to evaluate and control work practices to eliminate unnecessary exposure to ionizing radiation. The usefulness of the data produced however depends on its quality and traceability. The emphasis of the global dosimetry program is focused through the IAEA/WHO network of secondary standard dosimetry laboratories (SSDLs), which aims for the determination of SI quantities through proper traceable calibration of radiation protection equipment. The responsibility of SSDL-NUCLEAR MALAYSIA to guarantee a reliable dosimetry service, which is traceable to international standards, is elucidated. It acts as the basis for harmonized occupational radiation monitoring in Malaysia.

  4. Interfacing a biosurveillance portal and an international network of institutional analysts to detect biological threats.

    Science.gov (United States)

    Riccardo, Flavia; Shigematsu, Mika; Chow, Catherine; McKnight, C Jason; Linge, Jens; Doherty, Brian; Dente, Maria Grazia; Declich, Silvia; Barker, Mike; Barboza, Philippe; Vaillant, Laetitia; Donachie, Alastair; Mawudeku, Abla; Blench, Michael; Arthur, Ray

    2014-01-01

    The Early Alerting and Reporting (EAR) project, launched in 2008, is aimed at improving global early alerting and risk assessment and evaluating the feasibility and opportunity of integrating the analysis of biological, chemical, radionuclear (CBRN), and pandemic influenza threats. At a time when no international collaborations existed in the field of event-based surveillance, EAR's innovative approach involved both epidemic intelligence experts and internet-based biosurveillance system providers in the framework of an international collaboration called the Global Health Security Initiative, which involved the ministries of health of the G7 countries and Mexico, the World Health Organization, and the European Commission. The EAR project pooled data from 7 major internet-based biosurveillance systems onto a common portal that was progressively optimized for biological threat detection under the guidance of epidemic intelligence experts from public health institutions in Canada, the European Centre for Disease Prevention and Control, France, Germany, Italy, Japan, the United Kingdom, and the United States. The group became the first end users of the EAR portal, constituting a network of analysts working with a common standard operating procedure and risk assessment tools on a rotation basis to constantly screen and assess public information on the web for events that could suggest an intentional release of biological agents. Following the first 2-year pilot phase, the EAR project was tested in its capacity to monitor biological threats, proving that its working model was feasible and demonstrating the high commitment of the countries and international institutions involved. During the testing period, analysts using the EAR platform did not miss intentional events of a biological nature and did not issue false alarms. Through the findings of this initial assessment, this article provides insights into how the field of epidemic intelligence can advance through an

  5. Statistical assessment of crosstalk enrichment between gene groups in biological networks.

    Science.gov (United States)

    McCormack, Theodore; Frings, Oliver; Alexeyenko, Andrey; Sonnhammer, Erik L L

    2013-01-01

    Analyzing groups of functionally coupled genes or proteins in the context of global interaction networks has become an important aspect of bioinformatic investigations. Assessing the statistical significance of crosstalk enrichment between or within groups of genes can be a valuable tool for functional annotation of experimental gene sets. Here we present CrossTalkZ, a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. We demonstrate that the standard z-score is generally an appropriate and unbiased statistic. We further evaluate the ability of four different methods to reliably recover crosstalk within known biological pathways. We conclude that the methods preserving the second-order topological network properties perform best. Finally, we show how CrossTalkZ can be used to annotate experimental gene sets using known pathway annotations and that its performance at this task is superior to gene enrichment analysis (GEA). CrossTalkZ (available at http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/) is implemented in C++, easy to use, fast, accepts various input file formats, and produces a number of statistics. These include z-score, p-value, false discovery rate, and a test of normality for the null distributions.

  6. Logic-based models in systems biology: a predictive and parameter-free network analysis method.

    Science.gov (United States)

    Wynn, Michelle L; Consul, Nikita; Merajver, Sofia D; Schnell, Santiago

    2012-11-01

    Highly complex molecular networks, which play fundamental roles in almost all cellular processes, are known to be dysregulated in a number of diseases, most notably in cancer. As a consequence, there is a critical need to develop practical methodologies for constructing and analysing molecular networks at a systems level. Mathematical models built with continuous differential equations are an ideal methodology because they can provide a detailed picture of a network's dynamics. To be predictive, however, differential equation models require that numerous parameters be known a priori and this information is almost never available. An alternative dynamical approach is the use of discrete logic-based models that can provide a good approximation of the qualitative behaviour of a biochemical system without the burden of a large parameter space. Despite their advantages, there remains significant resistance to the use of logic-based models in biology. Here, we address some common concerns and provide a brief tutorial on the use of logic-based models, which we motivate with biological examples.

  7. Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World.

    Science.gov (United States)

    Di Silvestre, Dario; Bergamaschi, Andrea; Bellini, Edoardo; Mauri, PierLuigi

    2018-06-03

    The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

  8. A Network Biology Approach to Discover the Molecular Biomarker Associated with Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Liwei Zhuang

    2014-01-01

    Full Text Available In recent years, high throughput technologies such as microarray platform have provided a new avenue for hepatocellular carcinoma (HCC investigation. Traditionally, gene sets enrichment analysis of survival related genes is commonly used to reveal the underlying functional mechanisms. However, this approach usually produces too many candidate genes and cannot discover detailed signaling transduction cascades, which greatly limits their clinical application such as biomarker development. In this study, we have proposed a network biology approach to discover novel biomarkers from multidimensional omics data. This approach effectively combines clinical survival data with topological characteristics of human protein interaction networks and patients expression profiling data. It can produce novel network based biomarkers together with biological understanding of molecular mechanism. We have analyzed eighty HCC expression profiling arrays and identified that extracellular matrix and programmed cell death are the main themes related to HCC progression. Compared with traditional enrichment analysis, this approach can provide concrete and testable hypothesis on functional mechanism. Furthermore, the identified subnetworks can potentially be used as suitable targets for therapeutic intervention in HCC.

  9. Dosimetry in radioisotope placentography

    International Nuclear Information System (INIS)

    Sastry, K.G.K.; Reddy, A.R.; Nagaratnam, A.

    1976-01-01

    Radionuclide investigation of the placenta is being widely used in recent years for the diagnosis and management of vaginal bleeding in the third trimester of pregnancy. One is, therefore, concerned about the radiation exposure to the foetus during such procedures. In the present communication a precise method of estimation of radiation doses is presented. A concept termed 'effective absorbed dose constant' is utilized to enable the absorbed fractions and equilibrium absorbed dose constants to be more easily employed in radiation dose estimations. Tables of the effective absorbed dose constants for radionuclides like 131 I, 123 I, sup(113m)Tc, sup(99m)Tc, 67 Ga, and 51 Cr, are given for different masses and shapes. Masses of different organs of both mother and foetus at different periods of pregnancy and the biological turnover data for different radiopharmaceuticals are reviewed and typical values are presented. Radiation doses to different organs of both mother and foetus at the 30th week of pregnancy are finally estimated for 131 I-HSA, 123 I-SHA, sup(99m)Tc-HSA and sup(113m)In-chloride. The advantage of the effective absorbed dose constants in radiation dosimetry in general is discussed. The relative merits of different radiopharmaceuticals for placental investigations are brought out in comparison with antenatal pelvimetric and abdominal X-ray investigations, from the point of view of radiation doses. (author)

  10. Students Mental Representation of Biology Diagrams/Pictures Conventions Based on Formation of Causal Network

    Science.gov (United States)

    Sampurno, A. W.; Rahmat, A.; Diana, S.

    2017-09-01

    Diagrams/pictures conventions is one form of visual media that often used to assist students in understanding the biological concepts. The effectiveness of use diagrams/pictures in biology learning at school level has also been mostly reported. This study examines the ability of high school students in reading diagrams/pictures biological convention which is described by Mental Representation based on formation of causal networks. The study involved 30 students 11th grade MIA senior high school Banten Indonesia who are studying the excretory system. MR data obtained by Instrument worksheet, developed based on CNET-protocol, in which there are diagrams/drawings of nephron structure and urinary mechanism. Three patterns formed MR, namely Markov chain, feedback control with a single measurement, and repeated feedback control with multiple measurement. The third pattern is the most dominating pattern, differences in the pattern of MR reveal the difference in how and from which point the students begin to uncover important information contained in the diagram to establish a causal networks. Further analysis shows that a difference in the pattern of MR relate to how complex the students process the information contained in the diagrams/pictures.

  11. Endogenous Molecular-Cellular Network Cancer Theory: A Systems Biology Approach.

    Science.gov (United States)

    Wang, Gaowei; Yuan, Ruoshi; Zhu, Xiaomei; Ao, Ping

    2018-01-01

    In light of ever apparent limitation of the current dominant cancer mutation theory, a quantitative hypothesis for cancer genesis and progression, endogenous molecular-cellular network hypothesis has been proposed from the systems biology perspective, now for more than 10 years. It was intended to include both the genetic and epigenetic causes to understand cancer. Its development enters the stage of meaningful interaction with experimental and clinical data and the limitation of the traditional cancer mutation theory becomes more evident. Under this endogenous network hypothesis, we established a core working network of hepatocellular carcinoma (HCC) according to the hypothesis and quantified the working network by a nonlinear dynamical system. We showed that the two stable states of the working network reproduce the main known features of normal liver and HCC at both the modular and molecular levels. Using endogenous network hypothesis and validated working network, we explored genetic mutation pattern in cancer and potential strategies to cure or relieve HCC from a totally new perspective. Patterns of genetic mutations have been traditionally analyzed by posteriori statistical association approaches in light of traditional cancer mutation theory. One may wonder the possibility of a priori determination of any mutation regularity. Here, we found that based on the endogenous network theory the features of genetic mutations in cancers may be predicted without any prior knowledge of mutation propensities. Normal hepatocyte and cancerous hepatocyte stable states, specified by distinct patterns of expressions or activities of proteins in the network, provide means to directly identify a set of most probable genetic mutations and their effects in HCC. As the key proteins and main interactions in the network are conserved through cell types in an organism, similar mutational features may also be found in other cancers. This analysis yielded straightforward and testable

  12. International institute for collaborative cell biology and biochemistry--history and memoirs from an international network for biological sciences.

    Science.gov (United States)

    Cameron, L C

    2013-01-01

    I was invited to write this essay on the occasion of my selection as the recipient of the 2012 Bruce Alberts Award for Excellence in Science Education from the American Society for Cell Biology (ASCB). Receiving this award is an enormous honor. When I read the email announcement for the first time, it was more than a surprise to me, it was unbelievable. I joined ASCB in 1996, when I presented a poster and received a travel award. Since then, I have attended almost every ASCB meeting. I will try to use this essay to share with readers one of the best experiences in my life. Because this is an essay, I take the liberty of mixing some of my thoughts with data in a way that it not usual in scientific writing. I hope that this sacrifice of the format will achieve the goal of conveying what I have learned over the past 20 yr, during which time a group of colleagues and friends created a nexus of knowledge and wisdom. We have worked together to build a network capable of sharing and inspiring science all over the world.

  13. International Institute for Collaborative Cell Biology and Biochemistry—History and Memoirs from an International Network for Biological Sciences

    Science.gov (United States)

    Cameron, L. C.

    2013-01-01

    I was invited to write this essay on the occasion of my selection as the recipient of the 2012 Bruce Alberts Award for Excellence in Science Education from the American Society for Cell Biology (ASCB). Receiving this award is an enormous honor. When I read the email announcement for the first time, it was more than a surprise to me, it was unbelievable. I joined ASCB in 1996, when I presented a poster and received a travel award. Since then, I have attended almost every ASCB meeting. I will try to use this essay to share with readers one of the best experiences in my life. Because this is an essay, I take the liberty of mixing some of my thoughts with data in a way that it not usual in scientific writing. I hope that this sacrifice of the format will achieve the goal of conveying what I have learned over the past 20 yr, during which time a group of colleagues and friends created a nexus of knowledge and wisdom. We have worked together to build a network capable of sharing and inspiring science all over the world. PMID:24006381

  14. A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology

    NARCIS (Netherlands)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-01-01

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional

  15. Polymer gel dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Baldock, C [Institute of Medical Physics, School of Physics, University of Sydney (Australia); De Deene, Y [Radiotherapy and Nuclear Medicine, Ghent University Hospital (Belgium); Doran, S [CRUK Clinical Magnetic Resonance Research Group, Institute of Cancer Research, Surrey (United Kingdom); Ibbott, G [Radiation Physics, UT M D Anderson Cancer Center, Houston, TX (United States); Jirasek, A [Department of Physics and Astronomy, University of Victoria, Victoria, BC (Canada); Lepage, M [Centre d' imagerie moleculaire de Sherbrooke, Departement de medecine nucleaire et de radiobiologie, Universite de Sherbrooke, Sherbrooke, QC (Canada); McAuley, K B [Department of Chemical Engineering, Queen' s University, Kingston, ON (Canada); Oldham, M [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Schreiner, L J [Cancer Centre of South Eastern Ontario, Kingston, ON (Canada)], E-mail: c.baldock@physics.usyd.edu.au, E-mail: yves.dedeene@ugent.be

    2010-03-07

    Polymer gel dosimeters are fabricated f