A computational framework for bioimaging simulation

Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge in the mathematical form of biochemical reaction networks and understanding how higher level functions emerge from the combined action of biomolecules. However, there still remain formidable challenges in bridging the gap between bioimaging and mathematical modeling. Generally, measurements using fluorescence microscopy systems are influenced by systematic effects that arise from stochastic nature of biological cells, the imaging apparatus, and optical physics. Such systematic effects are always present in all bioimaging systems and hinder quantitative comparison between the cell model and bioimages. Computational tools for such a comparison are still unavailable. Thus, in this work, we present a computational framework for handling the parameters of the cell models and the optical physics governing bioimaging systems. Simulation using this framework can generate digital images of cell simulation results after accounting for the systematic effects. We then demonstrate that such a framework enables comparison at the level of photon-counting units.Comment: 57 page

FLUORESCENCE IN SITU HYBRIDIZATION (FISH) ENHANCEMENT USING MICROFLUIDIC FLOW FOR AN ACCURATE, FAST AND ECONOMICAL ASSESSMENT OF HER2 STATUS IN BREAST CANCER

The fluorescence in situ hybridization (FISH) is the gold standard in human epidermal growth factor receptor 2 (HER2) status assessment in breast cancer. The dissemination of the technique is impeded by the cost of reagents and long experimental time. For overcoming these limitations, we have developed a new method for implementing FISH for HER2 assessment for tissue analysis based on microfluidic technology

Upgrading of shielding for rare decay search in CANDLES

In the CANDLES experiment aiming to search for the very rare neutrino-less double beta decays (0νββ) using 48Ca, we introduced a new shielding system for high energy γ-rays from neutron captures in massive materials near the detector, in addition to the background reduction for 232Th decays in the 0νββ target of CaF2 crystals. The method of background reduction and the performance of newly installed shielding system are described

T2K neutrino flux prediction

cited By 15 art_number: 012001 affiliation: Centre for Particle Physics, Department of Physics, University of Alberta, Edmonton, AB, Canada; Albert Einstein Center for Fundamental Physics, Laboratory for High Energy Physics (LHEP), University of Bern, Bern, Switzerland; Department of Physics, Boston University, Boston, MA, United States; Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada; Department of Physics and Astronomy, University of California Irvine, Irvine, CA, United States; IRFU, CEA Saclay, Gif-sur-Yvette, France; Institute for Universe and Elementary Particles, Chonnam National University, Gwangju, South Korea; Department of Physics, University of Colorado at Boulder, Boulder, CO, United States; Department of Physics, Colorado State University, Fort Collins, CO, United States; Department of Physics, Dongshin University, Naju, South Korea; Department of Physics, Duke University, Durham, NC, United States; IN2P3-CNRS, Laboratoire Leprince-Ringuet, Ecole Polytechnique, Palaiseau, France; Institute for Particle Physics, ETH Zurich, Zurich, Switzerland; Section de Physique, DPNC, University of Geneva, Geneva, Switzerland; H. Niewodniczanski Institute of Nuclear Physics PAN, Cracow, Poland; High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan; Institut de Fisica d’Altes Energies (IFAE), Bellaterra (Barcelona), Spain; IFIC (CSIC and University of Valencia), Valencia, Spain; Department of Physics, Imperial College London, London, United Kingdom; INFN Sezione di Bari, Dipartimento Interuniversitario di Fisica, Università e Politecnico di Bari, Bari, Italy; INFN Sezione di Napoli and Dipartimento di Fisica, Università di Napoli, Napoli, Italy; INFN Sezione di Padova, Dipartimento di Fisica, Università di Padova, Padova, Italy; INFN Sezione di Roma, Università di Roma la Sapienza, Roma, Italy; Institute for Nuclear Research, Russian Academy of Sciences, Moscow, Russian Federation; Kobe University, Kobe, Japan; Department of Physics, Kyoto University, Kyoto, Japan; Physics Department, Lancaster University, Lancaster, United Kingdom; Department of Physics, University of Liverpool, Liverpool, United Kingdom; Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA, United States; Université de Lyon, Université Claude Bernard Lyon 1, IPN Lyon (IN2P3), Villeurbanne, France; Department of Physics, Miyagi University of Education, Sendai, Japan; National Centre for Nuclear Research, Warsaw, Poland; State University of New York at Stony Brook, Stony Brook, NY, United States; Department of Physics and Astronomy, Osaka City University, Department of Physics, Osaka, Japan; Department of Physics, Oxford University, Oxford, United Kingdom; UPMC, Université Paris Diderot, Laboratoire de Physique Nucléaire et de Hautes Energies (LPNHE), Paris, France; Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, United States; School of Physics, Queen Mary University of London, London, United Kingdom; Department of Physics, University of Regina, Regina, SK, Canada; Department of Physics and Astronomy, University of Rochester, Rochester, NY, United States; III. Physikalisches Institut, RWTH Aachen University, Aachen, Germany; Department of Physics and Astronomy, Seoul National University, Seoul, South Korea; Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom; University of Silesia, Institute of Physics, Katowice, Poland; STFC, Rutherford Appleton Laboratory, Harwell Oxford, Warrington, United Kingdom; Department of Physics, University of Tokyo, Tokyo, Japan; Institute for Cosmic Ray Research, Kamioka Observatory, University of Tokyo, Kamioka, Japan; Institute for Cosmic Ray Research, Research Center for Cosmic Neutrinos, University of Tokyo, Kashiwa, Japan; Department of Physics, University of Toronto, Toronto, ON, Canada; TRIUMF, Vancouver, BC, Canada; Department of Physics and Astronomy, University of Victoria, Victoria, BC, Canada; Faculty of Physics, University of Warsaw, Warsaw, Poland; Institute of Radioelectronics, Warsaw University of Technology, Warsaw, Poland; Department of Physics, University of Warwick, Coventry, United Kingdom; Department of Physics, University of Washington, Seattle, WA, United States; Department of Physics, University of Winnipeg, Winnipeg, MB, Canada; Faculty of Physics and Astronomy, Wroclaw University, Wroclaw, Poland; Department of Physics and Astronomy, York University, Toronto, ON, Canada references: Astier, P., (2003) Nucl. Instrum. Methods Phys. Res., Sect. A, 515, p. 800. , (NOMAD Collaboration), NIMAER 0168-9002 10.1016/j.nima.2003.07.054; Ahn, M., (2006) Phys. Rev. D, 74, p. 072003. , (K2K Collaboration), PRVDAQ 1550-7998 10.1103/PhysRevD.74.072003; Adamson, P., (2008) Phys. Rev. D, 77, p. 072002. , (MINOS Collaboration), PRVDAQ 1550-7998 10.1103/PhysRevD.77.072002; Aguilar-Arevalo, A., (2009) Phys. Rev. D, 79, p. 072002. , (MiniBooNE Collaboration), PRVDAQ 1550-7998 10.1103/PhysRevD.79.072002; (2003) Letter of Intent: Neutrino Oscillation Experiment at JHF, , http://neutrino.kek.jp/jhfnu/loi/loi_JHFcor.pdf, T2K Collaboration; Abe, K., (2011) Nucl. Instrum. Methods Phys. Res., Sect. A, 659, p. 106. , (T2K Collaboration), NIMAER 0168-9002 10.1016/j.nima.2011.06.067; Abe, K., (2011) Phys. Rev. Lett., 107, p. 041801. , (T2K Collaboration), PRLTAO 0031-9007 10.1103/PhysRevLett.107.041801; Abe, K., (2012) Phys. Rev. D, 85, p. 031103. , (T2K Collaboration), PRVDAQ 1550-7998 10.1103/PhysRevD.85.031103; Fukuda, Y., (2003) Nucl. Instrum. Methods Phys. Res., Sect. A, 501, p. 418. , NIMAER 0168-9002 10.1016/S0168-9002(03)00425-X; Beavis, D., Carroll, A., Chiang, I., (1995), Physics Design Report, BNL 52459Abgrall, N., (2011) Phys. Rev. C, 84, p. 034604. , (NA61/SHINE Collaboration), PRVCAN 0556-2813 10.1103/PhysRevC.84.034604; Abgrall, N., (2012) Phys. Rev. C, 85, p. 035210. , (NA61/SHINE Collaboration), PRVCAN 0556-2813 10.1103/PhysRevC.85.035210; Bhadra, S., (2013) Nucl. Instrum. Methods Phys. Res., Sect. A, 703, p. 45. , NIMAER 0168-9002 10.1016/j.nima.2012.11.044; Van Der Meer, S., Report No. CERN-61-07Palmer, R., Report No. CERN-65-32, 141Ichikawa, A., (2012) Nucl. Instrum. Methods Phys. Res., Sect. A, 690, p. 27. , NIMAER 0168-9002 10.1016/j.nima.2012.06.045; Matsuoka, K., (2010) Nucl. Instrum. Methods Phys. Res., Sect. A, 624, p. 591. , NIMAER 0168-9002 10.1016/j.nima.2010.09.074; Abe, K., (2012) Nucl. Instrum. Methods Phys. Res., Sect. A, 694, p. 211. , (T2K Collaboration), NIMAER 0168-9002 10.1016/j.nima.2012.03.023; Abgrall, N., (2011) Nucl. Instrum. Methods Phys. Res., Sect. A, 637, p. 25. , (T2K ND280 TPC Collaboration), NIMAER 0168-9002 10.1016/j.nima.2011.02. 036; Amaudruz, P.-A., (2012) Nucl. Instrum. Methods Phys. Res., Sect. A, 696, p. 1. , (T2K ND280 FGD Collaboration), NIMAER 0168-9002 10.1016/j.nima.2012.08. 020; Battistoni, G., Cerutti, F., Fasso, A., Ferrari, A., Muraro, S., Ranft, J., Roesler, S., Sala, P.R., (2007) AIP Conf. Proc., 896, p. 31. , APCPCS 0094-243X 10.1063/1.2720455; A. Ferrari, P. R. Sala, A. Fasso, and J. Ranft, Report No. CERN-2005-010A. Ferrari P. R. Sala A. Fasso J. Ranft Report No. SLAC-R-773A. Ferrari P. R. Sala A. Fasso J. Ranft Report No. INFN-TC-05-11R. Brun, F. Carminati, and S. Giani, Report No. CERN-W5013Zeitnitz, C., Gabriel, T.A., (1993) Proceedings of International Conference on Calorimetry in High Energy Physics, , in Elsevier Science B.V., Tallahassee, FL; Fasso, A., Ferrari, A., Ranft, J., Sala, P.R., Proceedings of the International Conference on Calorimetry in High Energy Physics, 1994, , in; Beringer, J., (2012) Phys. Rev. D, 86, p. 010001. , (Particle Data Group), PRVDAQ 1550-7998 10.1103/PhysRevD.86.010001; Eichten, T., (1972) Nucl. Phys. B, 44, p. 333. , NUPBBO 0550-3213 10.1016/0550-3213(72)90120-4; Allaby, J.V., Tech. Rep. 70-12 (CERN, 1970)Chemakin, I., (2008) Phys. Rev. C, 77, p. 015209. , PRVCAN 0556-2813 10.1103/PhysRevC.77.015209; Abrams, R.J., Cool, R., Giacomelli, G., Kycia, T., Leontic, B., Li, K., Michael, D., (1970) Phys. Rev. D, 1, p. 1917. , PRVDAQ 0556-2821 10.1103/PhysRevD.1.1917; Allaby, J.V., (1970) Yad. Fiz., 12, p. 538. , IDFZA7 0044-0027; Allaby, J.V., (1969) Phys. Lett. B, 30, p. 500. , PYLBAJ 0370-2693 10.1016/0370-2693(69)90184-1; Allardyce, B.W., (1973) Nucl. Phys. A, 209, p. 1. , NUPABL 0375-9474 10.1016/0375-9474(73)90049-3; Bellettini, G., Cocconi, G., Diddens, A.N., Lillethun, E., Matthiae, G., Scanlon, J.P., Wetherell, A.M., (1966) Nucl. Phys., 79, p. 609. , NUPHA7 0029-5582 10.1016/0029-5582(66)90267-7; Bobchenko, B.M., (1979) Sov. J. Nucl. Phys., 30, p. 805. , SJNCAS 0038-5506; Carroll, A.S., (1979) Phys. Lett. B, 80, p. 319. , PYLBAJ 0370-2693 10.1016/0370-2693(79)90226-0; Cronin, J.W., Cool, R., Abashian, A., (1957) Phys. Rev., 107, p. 1121. , PHRVAO 0031-899X 10.1103/PhysRev.107.1121; Chen, F.F., Leavitt, C., Shapiro, A., (1955) Phys. Rev., 99, p. 857. , PHRVAO 0031-899X 10.1103/PhysRev.99.857; Denisov, S.P., Donskov, S.V., Gorin, Yu.P., Krasnokutsky, R.N., Petrukhin, A.I., Prokoshkin, Yu.D., Stoyanova, D.A., (1973) Nucl. Phys. B, 61, p. 62. , NUPBBO 0550-3213 10.1016/0550-3213(73)90351-9; Longo, M.J., Moyer, B.J., (1962) Phys. Rev., 125, p. 701. , PHRVAO 0031-899X 10.1103/PhysRev.125.701; Vlasov, A.V., (1978) Sov. J. Nucl. Phys., 27, p. 222. , SJNCAS 0038-5506; Feynman, R., (1969) Phys. Rev. Lett., 23, p. 1415. , PRLTAO 0031-9007 10.1103/PhysRevLett.23.1415; Bonesini, M., Marchionni, A., Pietropaolo, F., Tabarelli De Fatis, T., (2001) Eur. Phys. J. C, 20, p. 13. , EPCFFB 1434-6044 10.1007/s100520100656; Barton, D.S., (1983) Phys. Rev. D, 27, p. 2580. , PRVDAQ 0556-2821 10.1103/PhysRevD.27.2580; Skubic, P., (1978) Phys. Rev. D, 18, p. 3115. , PRVDAQ 0556-2821 10.1103/PhysRevD.18.3115; Feynman, R.P., (1972) Photon-Hadron Interactions, , Benjamin, New York; Bjorken, J.D., Paschos, E.A., (1969) Phys. Rev., 185, p. 1975. , PHRVAO 0031-899X 10.1103/PhysRev.185.1975; Taylor, F.E., Carey, D., Johnson, J., Kammerud, R., Ritchie, D., Roberts, A., Sauer, J., Walker, J., (1976) Phys. Rev. D, 14, p. 1217. , PRVDAQ 0556-2821 10.1103/PhysRevD.14.1217; Abgrall, N., (2013) Nucl. Instrum. Methods Phys. Res., Sect. A, 701, p. 99. , NIMAER 0168-9002 10.1016/j.nima.2012.10.079; Hayato, Y., (2002) Nucl. Phys. B, Proc. Suppl., 112, p. 171. , NPBSE7 0920-5632 10.1016/S0920-5632(02)01759-0 correspondence_address1: Abe, K.; Institute for Cosmic Ray Research, Kamioka Observatory, University of Tokyo, Kamioka, Japan coden: PRVDA abbrev_source_title: Phys Rev D Part Fields Gravit Cosmol document_type: Article source: Scopu

First muon-neutrino disappearance study with an off-axis beam

We report a measurement of muon-neutrino disappearance in the T2K experiment. The 295-km muon-neutrino beam from Tokai to Kamioka is the first implementation of the off-axis technique in a long-baseline neutrino oscillation experiment

Traffic management project in Phnom Penh

Traffic congestion and accidents are major issues in Phnom Penh, the capital city of the Kingdom of Cambodia. An inefficient signal system and lack of traffic discipline contributed to the unfavorable traffic conditions. A comprehensive traffic management project was recently implemented. An area traffic control system that controls traffic signals in the city based on the traffic conditions was introduced, and other traffic management improvement works such as pavement markings, traffic signs, and median dividers were installed. The project is making a positive impact on road users. Efficient operation and maintenance are key factors for the project to sustain its benefits. Keywords: Traffic management, Traffic signal, Area traffic control, Congestion, Adaptive contro

Involvement of iron-evoked oxidative stress in smoking-related endothelial dysfunction in healthy young men.

BACKGROUND: Oxidative stress and smoking contribute to endothelial dysfunction. Iron might also play a role in oxidative stress generation and endothelial dysfunction. However, the involvement of iron in smoking-induced endothelial dysfunction in healthy smokers remains unclear. Therefore, we examined here whether (1) intravenous iron infusion impaired endothelial function evaluated by flow-mediated vasodilatation (FMD) in non-smokers, and (2) deferoxamine, a potent iron chelator, ameliorated endothelial dysfunction in healthy smokers. METHODS: Eight healthy young male non-smokers (23 ± 4 years old) received intravenous injection of saccharated ferric oxide (0.7 mg/kg body weight), while 10 age-matched healthy male smokers received deferoxamine mesylate (8.3 mg/kg body weight). At baseline, 5 and 20 minutes after treatment with iron or deferoxamine, biochemical variables were measured, including serum iron and marondialdehyde (MDA), a marker of lipid oxidation, and endothelial function was simultaneously evaluated by FMD. RESULTS: Compared with non-smokers, FMD was significantly lower in smokers. Iron and MDA levels were significantly increased, whereas FMD was impaired by iron infusion in non-smokers. Conversely, deferoxamine treatment significantly decreased iron and MDA levels and restored the decreased FMD in smokers. Baseline serum iron and MDA levels in all 18 subjects (non-smokers and smokers) were correlated with each other. There was a significant inverse correlation between the changes in MDA values and FMD from baseline in 18 men. Endothelium-independent vasodilation by glyceryl trinitrate was unaltered by either treatment. CONCLUSIONS: Our present study suggests that iron-evoked oxidative stress might play a role in endothelial dysfunction in healthy smokers